2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AlignmentUtils;
25 import jalview.analysis.CrossRef;
26 import jalview.analysis.Dna;
27 import jalview.analysis.GeneticCodeI;
28 import jalview.analysis.ParseProperties;
29 import jalview.analysis.SequenceIdMatcher;
30 import jalview.api.AlignExportSettingsI;
31 import jalview.api.AlignViewControllerGuiI;
32 import jalview.api.AlignViewControllerI;
33 import jalview.api.AlignViewportI;
34 import jalview.api.AlignmentViewPanel;
35 import jalview.api.FeatureSettingsControllerI;
36 import jalview.api.FeatureSettingsModelI;
37 import jalview.api.SplitContainerI;
38 import jalview.api.ViewStyleI;
39 import jalview.api.analysis.SimilarityParamsI;
40 import jalview.bin.Cache;
41 import jalview.bin.Jalview;
42 import jalview.commands.CommandI;
43 import jalview.commands.EditCommand;
44 import jalview.commands.EditCommand.Action;
45 import jalview.commands.OrderCommand;
46 import jalview.commands.RemoveGapColCommand;
47 import jalview.commands.RemoveGapsCommand;
48 import jalview.commands.SlideSequencesCommand;
49 import jalview.commands.TrimRegionCommand;
50 import jalview.datamodel.AlignExportSettingsAdapter;
51 import jalview.datamodel.AlignedCodonFrame;
52 import jalview.datamodel.Alignment;
53 import jalview.datamodel.AlignmentAnnotation;
54 import jalview.datamodel.AlignmentExportData;
55 import jalview.datamodel.AlignmentI;
56 import jalview.datamodel.AlignmentOrder;
57 import jalview.datamodel.AlignmentView;
58 import jalview.datamodel.ColumnSelection;
59 import jalview.datamodel.HiddenColumns;
60 import jalview.datamodel.PDBEntry;
61 import jalview.datamodel.SeqCigar;
62 import jalview.datamodel.Sequence;
63 import jalview.datamodel.SequenceGroup;
64 import jalview.datamodel.SequenceI;
65 import jalview.gui.ColourMenuHelper.ColourChangeListener;
66 import jalview.gui.ViewSelectionMenu.ViewSetProvider;
67 import jalview.io.AlignmentProperties;
68 import jalview.io.AnnotationFile;
69 import jalview.io.BackupFiles;
70 import jalview.io.BioJsHTMLOutput;
71 import jalview.io.DataSourceType;
72 import jalview.io.FileFormat;
73 import jalview.io.FileFormatI;
74 import jalview.io.FileFormats;
75 import jalview.io.FileLoader;
76 import jalview.io.FileParse;
77 import jalview.io.FormatAdapter;
78 import jalview.io.HtmlSvgOutput;
79 import jalview.io.IdentifyFile;
80 import jalview.io.JPredFile;
81 import jalview.io.JalviewFileChooser;
82 import jalview.io.JalviewFileView;
83 import jalview.io.JnetAnnotationMaker;
84 import jalview.io.NewickFile;
85 import jalview.io.ScoreMatrixFile;
86 import jalview.io.TCoffeeScoreFile;
87 import jalview.io.vcf.VCFLoader;
88 import jalview.jbgui.GAlignFrame;
89 import jalview.project.Jalview2XML;
90 import jalview.schemes.ColourSchemeI;
91 import jalview.schemes.ColourSchemes;
92 import jalview.schemes.ResidueColourScheme;
93 import jalview.schemes.TCoffeeColourScheme;
94 import jalview.util.ImageMaker.TYPE;
95 import jalview.util.MessageManager;
96 import jalview.util.Platform;
97 import jalview.viewmodel.AlignmentViewport;
98 import jalview.viewmodel.ViewportRanges;
99 import jalview.ws.DBRefFetcher;
100 import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
101 import jalview.ws.jws1.Discoverer;
102 import jalview.ws.jws2.Jws2Discoverer;
103 import jalview.ws.jws2.jabaws2.Jws2Instance;
104 import jalview.ws.seqfetcher.DbSourceProxy;
106 import java.awt.BorderLayout;
107 import java.awt.Color;
108 import java.awt.Component;
109 import java.awt.Rectangle;
110 import java.awt.Toolkit;
111 import java.awt.datatransfer.Clipboard;
112 import java.awt.datatransfer.DataFlavor;
113 import java.awt.datatransfer.StringSelection;
114 import java.awt.datatransfer.Transferable;
115 import java.awt.dnd.DnDConstants;
116 import java.awt.dnd.DropTargetDragEvent;
117 import java.awt.dnd.DropTargetDropEvent;
118 import java.awt.dnd.DropTargetEvent;
119 import java.awt.dnd.DropTargetListener;
120 import java.awt.event.ActionEvent;
121 import java.awt.event.ActionListener;
122 import java.awt.event.FocusAdapter;
123 import java.awt.event.FocusEvent;
124 import java.awt.event.ItemEvent;
125 import java.awt.event.ItemListener;
126 import java.awt.event.KeyAdapter;
127 import java.awt.event.KeyEvent;
128 import java.awt.event.MouseEvent;
129 import java.awt.print.PageFormat;
130 import java.awt.print.PrinterJob;
131 import java.beans.PropertyChangeEvent;
133 import java.io.FileWriter;
134 import java.io.PrintWriter;
136 import java.util.ArrayList;
137 import java.util.Arrays;
138 import java.util.Deque;
139 import java.util.Enumeration;
140 import java.util.Hashtable;
141 import java.util.List;
142 import java.util.Vector;
144 import javax.swing.ButtonGroup;
145 import javax.swing.JCheckBoxMenuItem;
146 import javax.swing.JComponent;
147 import javax.swing.JEditorPane;
148 import javax.swing.JInternalFrame;
149 import javax.swing.JLabel;
150 import javax.swing.JLayeredPane;
151 import javax.swing.JMenu;
152 import javax.swing.JMenuItem;
153 import javax.swing.JPanel;
154 import javax.swing.JScrollPane;
155 import javax.swing.SwingUtilities;
157 import ext.vamsas.ServiceHandle;
163 * @version $Revision$
165 @SuppressWarnings("serial")
166 public class AlignFrame extends GAlignFrame implements DropTargetListener,
167 IProgressIndicator, AlignViewControllerGuiI, ColourChangeListener
170 public static final int DEFAULT_WIDTH = 700;
172 public static final int DEFAULT_HEIGHT = 500;
175 * The currently displayed panel (selected tabbed view if more than one)
177 public AlignmentPanel alignPanel;
179 AlignViewport viewport;
181 public AlignViewControllerI avc;
183 List<AlignmentPanel> alignPanels = new ArrayList<>();
186 * Last format used to load or save alignments in this window
188 FileFormatI currentFileFormat = null;
191 * Current filename for this alignment
193 String fileName = null;
198 * Creates a new AlignFrame object with specific width and height.
204 public AlignFrame(AlignmentI al, int width, int height)
206 this(al, null, width, height);
210 * Creates a new AlignFrame object with specific width, height and
216 * @param sequenceSetId
218 public AlignFrame(AlignmentI al, int width, int height,
219 String sequenceSetId)
221 this(al, null, width, height, sequenceSetId);
225 * Creates a new AlignFrame object with specific width, height and
231 * @param sequenceSetId
234 public AlignFrame(AlignmentI al, int width, int height,
235 String sequenceSetId, String viewId)
237 this(al, null, width, height, sequenceSetId, viewId);
241 * new alignment window with hidden columns
245 * @param hiddenColumns
246 * ColumnSelection or null
248 * Width of alignment frame
252 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
255 this(al, hiddenColumns, width, height, null);
259 * Create alignment frame for al with hiddenColumns, a specific width and
260 * height, and specific sequenceId
263 * @param hiddenColumns
266 * @param sequenceSetId
269 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
270 int height, String sequenceSetId)
272 this(al, hiddenColumns, width, height, sequenceSetId, null);
276 * Create alignment frame for al with hiddenColumns, a specific width and
277 * height, and specific sequenceId
280 * @param hiddenColumns
283 * @param sequenceSetId
288 public AlignFrame(AlignmentI al, HiddenColumns hiddenColumns, int width,
289 int height, String sequenceSetId, String viewId)
291 setSize(width, height);
293 if (al.getDataset() == null)
298 viewport = new AlignViewport(al, hiddenColumns, sequenceSetId, viewId);
300 alignPanel = new AlignmentPanel(this, viewport);
302 addAlignmentPanel(alignPanel, true);
306 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
307 HiddenColumns hiddenColumns, int width, int height)
309 setSize(width, height);
311 if (al.getDataset() == null)
316 viewport = new AlignViewport(al, hiddenColumns);
318 if (hiddenSeqs != null && hiddenSeqs.length > 0)
320 viewport.hideSequence(hiddenSeqs);
322 alignPanel = new AlignmentPanel(this, viewport);
323 addAlignmentPanel(alignPanel, true);
328 * Make a new AlignFrame from existing alignmentPanels
335 public AlignFrame(AlignmentPanel ap)
339 addAlignmentPanel(ap, false);
344 * initalise the alignframe from the underlying viewport data and the
349 // setBackground(Color.white); // BH 2019
351 if (!Jalview.isHeadlessMode())
353 progressBar = new ProgressBar(this.statusPanel, this.statusBar);
356 avc = new jalview.controller.AlignViewController(this, viewport,
358 if (viewport.getAlignmentConservationAnnotation() == null)
360 // BLOSUM62Colour.setEnabled(false);
361 conservationMenuItem.setEnabled(false);
362 modifyConservation.setEnabled(false);
363 // PIDColour.setEnabled(false);
364 // abovePIDThreshold.setEnabled(false);
365 // modifyPID.setEnabled(false);
368 String sortby = jalview.bin.Cache.getDefault("SORT_ALIGNMENT",
371 if (sortby.equals("Id"))
373 sortIDMenuItem_actionPerformed(null);
375 else if (sortby.equals("Pairwise Identity"))
377 sortPairwiseMenuItem_actionPerformed(null);
381 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
383 setMenusFromViewport(viewport);
384 buildSortByAnnotationScoresMenu();
385 calculateTree.addActionListener(new ActionListener()
389 public void actionPerformed(ActionEvent e)
396 if (Desktop.desktop != null)
398 this.setDropTarget(new java.awt.dnd.DropTarget(this, this));
399 if (!Platform.isJS())
401 addServiceListeners();
406 if (viewport.getWrapAlignment())
408 wrapMenuItem_actionPerformed(null);
411 if (jalview.bin.Cache.getDefault("SHOW_OVERVIEW", false))
413 this.overviewMenuItem_actionPerformed(null);
418 final List<AlignmentPanel> selviews = new ArrayList<>();
419 final List<AlignmentPanel> origview = new ArrayList<>();
420 final String menuLabel = MessageManager
421 .getString("label.copy_format_from");
422 ViewSelectionMenu vsel = new ViewSelectionMenu(menuLabel,
423 new ViewSetProvider()
427 public AlignmentPanel[] getAllAlignmentPanels()
430 origview.add(alignPanel);
431 // make an array of all alignment panels except for this one
432 List<AlignmentPanel> aps = new ArrayList<>(
433 Arrays.asList(Desktop.getAlignmentPanels(null)));
434 aps.remove(AlignFrame.this.alignPanel);
435 return aps.toArray(new AlignmentPanel[aps.size()]);
437 }, selviews, new ItemListener()
441 public void itemStateChanged(ItemEvent e)
443 if (origview.size() > 0)
445 final AlignmentPanel ap = origview.get(0);
448 * Copy the ViewStyle of the selected panel to 'this one'.
449 * Don't change value of 'scaleProteinAsCdna' unless copying
452 ViewStyleI vs = selviews.get(0).getAlignViewport()
454 boolean fromSplitFrame = selviews.get(0)
455 .getAlignViewport().getCodingComplement() != null;
458 vs.setScaleProteinAsCdna(ap.getAlignViewport()
459 .getViewStyle().isScaleProteinAsCdna());
461 ap.getAlignViewport().setViewStyle(vs);
464 * Also rescale ViewStyle of SplitFrame complement if there is
465 * one _and_ it is set to 'scaledProteinAsCdna'; we don't copy
466 * the whole ViewStyle (allow cDNA protein to have different
469 AlignViewportI complement = ap.getAlignViewport()
470 .getCodingComplement();
471 if (complement != null && vs.isScaleProteinAsCdna())
473 AlignFrame af = Desktop.getAlignFrameFor(complement);
474 ((SplitFrame) af.getSplitViewContainer())
476 af.setMenusForViewport();
480 ap.setSelected(true);
481 ap.alignFrame.setMenusForViewport();
486 if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
487 .indexOf("devel") > -1
488 || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
489 .indexOf("test") > -1)
491 formatMenu.add(vsel);
493 addFocusListener(new FocusAdapter()
496 public void focusGained(FocusEvent e)
498 Jalview.setCurrentAlignFrame(AlignFrame.this);
505 * Change the filename and format for the alignment, and enable the 'reload'
506 * button functionality.
513 public void setFileName(String file, FileFormatI format)
516 setFileFormat(format);
517 reload.setEnabled(true);
521 * JavaScript will have this, maybe others. More dependable than a file name
522 * and maintains a reference to the actual bytes loaded.
526 public void setFileObject(File file)
528 this.fileObject = file;
532 * Add a KeyListener with handlers for various KeyPressed and KeyReleased
535 void addKeyListener()
537 addKeyListener(new KeyAdapter()
540 public void keyPressed(KeyEvent evt)
542 if (viewport.cursorMode
543 && ((evt.getKeyCode() >= KeyEvent.VK_0
544 && evt.getKeyCode() <= KeyEvent.VK_9)
545 || (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0
546 && evt.getKeyCode() <= KeyEvent.VK_NUMPAD9))
547 && Character.isDigit(evt.getKeyChar()))
549 alignPanel.getSeqPanel().numberPressed(evt.getKeyChar());
552 switch (evt.getKeyCode())
555 case 27: // escape key
556 deselectAllSequenceMenuItem_actionPerformed(null);
560 case KeyEvent.VK_DOWN:
561 if (evt.isAltDown() || !viewport.cursorMode)
563 moveSelectedSequences(false);
565 if (viewport.cursorMode)
567 alignPanel.getSeqPanel().moveCursor(0, 1);
572 if (evt.isAltDown() || !viewport.cursorMode)
574 moveSelectedSequences(true);
576 if (viewport.cursorMode)
578 alignPanel.getSeqPanel().moveCursor(0, -1);
583 case KeyEvent.VK_LEFT:
584 if (evt.isAltDown() || !viewport.cursorMode)
586 slideSequences(false,
587 alignPanel.getSeqPanel().getKeyboardNo1());
591 alignPanel.getSeqPanel().moveCursor(-1, 0);
596 case KeyEvent.VK_RIGHT:
597 if (evt.isAltDown() || !viewport.cursorMode)
599 slideSequences(true, alignPanel.getSeqPanel().getKeyboardNo1());
603 alignPanel.getSeqPanel().moveCursor(1, 0);
607 case KeyEvent.VK_SPACE:
608 if (viewport.cursorMode)
610 alignPanel.getSeqPanel().insertGapAtCursor(evt.isControlDown()
611 || evt.isShiftDown() || evt.isAltDown());
615 // case KeyEvent.VK_A:
616 // if (viewport.cursorMode)
618 // alignPanel.seqPanel.insertNucAtCursor(false,"A");
619 // //System.out.println("A");
623 * case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
624 * System.out.println("closing bracket"); } break;
626 case KeyEvent.VK_DELETE:
627 case KeyEvent.VK_BACK_SPACE:
628 if (!viewport.cursorMode)
630 cut_actionPerformed();
634 alignPanel.getSeqPanel().deleteGapAtCursor(evt.isControlDown()
635 || evt.isShiftDown() || evt.isAltDown());
641 if (viewport.cursorMode)
643 alignPanel.getSeqPanel().setCursorRow();
647 if (viewport.cursorMode && !evt.isControlDown())
649 alignPanel.getSeqPanel().setCursorColumn();
653 if (viewport.cursorMode)
655 alignPanel.getSeqPanel().setCursorPosition();
659 case KeyEvent.VK_ENTER:
660 case KeyEvent.VK_COMMA:
661 if (viewport.cursorMode)
663 alignPanel.getSeqPanel().setCursorRowAndColumn();
668 if (viewport.cursorMode)
670 alignPanel.getSeqPanel().setSelectionAreaAtCursor(true);
674 if (viewport.cursorMode)
676 alignPanel.getSeqPanel().setSelectionAreaAtCursor(false);
681 viewport.cursorMode = !viewport.cursorMode;
682 setStatus(MessageManager
683 .formatMessage("label.keyboard_editing_mode", new String[]
684 { (viewport.cursorMode ? "on" : "off") }));
685 if (viewport.cursorMode)
687 ViewportRanges ranges = viewport.getRanges();
688 alignPanel.getSeqPanel().seqCanvas.cursorX = ranges
690 alignPanel.getSeqPanel().seqCanvas.cursorY = ranges
693 alignPanel.getSeqPanel().seqCanvas.repaint();
699 Help.showHelpWindow();
700 } catch (Exception ex)
702 ex.printStackTrace();
707 boolean toggleSeqs = !evt.isControlDown();
708 boolean toggleCols = !evt.isShiftDown();
709 toggleHiddenRegions(toggleSeqs, toggleCols);
714 boolean toggleSel = evt.isControlDown() || evt.isMetaDown();
715 boolean modifyExisting = true; // always modify, don't clear
716 // evt.isShiftDown();
717 boolean invertHighlighted = evt.isAltDown();
718 avc.markHighlightedColumns(invertHighlighted, modifyExisting,
722 case KeyEvent.VK_PAGE_UP:
723 viewport.getRanges().pageUp();
725 case KeyEvent.VK_PAGE_DOWN:
726 viewport.getRanges().pageDown();
732 public void keyReleased(KeyEvent evt)
734 switch (evt.getKeyCode())
736 case KeyEvent.VK_LEFT:
737 if (evt.isAltDown() || !viewport.cursorMode)
739 viewport.firePropertyChange("alignment", null,
740 viewport.getAlignment().getSequences());
744 case KeyEvent.VK_RIGHT:
745 if (evt.isAltDown() || !viewport.cursorMode)
747 viewport.firePropertyChange("alignment", null,
748 viewport.getAlignment().getSequences());
756 public void addAlignmentPanel(final AlignmentPanel ap, boolean newPanel)
758 ap.alignFrame = this;
759 avc = new jalview.controller.AlignViewController(this, viewport,
764 PaintRefresher.Register(ap, ap.av.getSequenceSetId());
766 int aSize = alignPanels.size();
768 tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
770 if (aSize == 1 && ap.av.getViewName() == null)
772 this.getContentPane().add(ap, BorderLayout.CENTER);
778 setInitialTabVisible();
781 expandViews.setEnabled(true);
782 gatherViews.setEnabled(true);
783 tabbedPane.addTab(ap.av.getViewName(), ap);
785 ap.setVisible(false);
790 if (ap.av.isPadGaps())
792 ap.av.getAlignment().padGaps();
794 ap.av.updateConservation(ap);
795 ap.av.updateConsensus(ap);
796 ap.av.updateStrucConsensus(ap);
800 public void setInitialTabVisible()
802 expandViews.setEnabled(true);
803 gatherViews.setEnabled(true);
804 tabbedPane.setVisible(true);
805 AlignmentPanel first = alignPanels.get(0);
806 tabbedPane.addTab(first.av.getViewName(), first);
807 this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
810 public AlignViewport getViewport()
815 /* Set up intrinsic listeners for dynamically generated GUI bits. */
816 private void addServiceListeners()
818 final java.beans.PropertyChangeListener thisListener;
819 Desktop.instance.addJalviewPropertyChangeListener("services",
820 thisListener = new java.beans.PropertyChangeListener()
823 public void propertyChange(PropertyChangeEvent evt)
825 // // System.out.println("Discoverer property change.");
826 // if (evt.getPropertyName().equals("services"))
828 SwingUtilities.invokeLater(new Runnable()
835 "Rebuild WS Menu for service change");
836 BuildWebServiceMenu();
843 addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
846 public void internalFrameClosed(
847 javax.swing.event.InternalFrameEvent evt)
849 // System.out.println("deregistering discoverer listener");
850 Desktop.instance.removeJalviewPropertyChangeListener("services",
852 closeMenuItem_actionPerformed(true);
855 // Finally, build the menu once to get current service state
856 new Thread(new Runnable()
861 BuildWebServiceMenu();
867 * Configure menu items that vary according to whether the alignment is
868 * nucleotide or protein
870 public void setGUINucleotide()
872 AlignmentI al = getViewport().getAlignment();
873 boolean nucleotide = al.isNucleotide();
875 loadVcf.setVisible(nucleotide);
876 showTranslation.setVisible(nucleotide);
877 showReverse.setVisible(nucleotide);
878 showReverseComplement.setVisible(nucleotide);
879 conservationMenuItem.setEnabled(!nucleotide);
881 .setEnabled(!nucleotide && conservationMenuItem.isSelected());
882 showGroupConservation.setEnabled(!nucleotide);
884 showComplementMenuItem
885 .setText(nucleotide ? MessageManager.getString("label.protein")
886 : MessageManager.getString("label.nucleotide"));
890 * set up menus for the current viewport. This may be called after any
891 * operation that affects the data in the current view (selection changed,
892 * etc) to update the menus to reflect the new state.
895 public void setMenusForViewport()
897 setMenusFromViewport(viewport);
901 * Need to call this method when tabs are selected for multiple views, or when
902 * loading from Jalview2XML.java
907 public void setMenusFromViewport(AlignViewport av)
909 padGapsMenuitem.setSelected(av.isPadGaps());
910 colourTextMenuItem.setSelected(av.isShowColourText());
911 abovePIDThreshold.setSelected(av.getAbovePIDThreshold());
912 modifyPID.setEnabled(abovePIDThreshold.isSelected());
913 conservationMenuItem.setSelected(av.getConservationSelected());
914 modifyConservation.setEnabled(conservationMenuItem.isSelected());
915 seqLimits.setSelected(av.getShowJVSuffix());
916 idRightAlign.setSelected(av.isRightAlignIds());
917 centreColumnLabelsMenuItem.setState(av.isCentreColumnLabels());
918 renderGapsMenuItem.setSelected(av.isRenderGaps());
919 wrapMenuItem.setSelected(av.getWrapAlignment());
920 scaleAbove.setVisible(av.getWrapAlignment());
921 scaleLeft.setVisible(av.getWrapAlignment());
922 scaleRight.setVisible(av.getWrapAlignment());
923 annotationPanelMenuItem.setState(av.isShowAnnotation());
925 * Show/hide annotations only enabled if annotation panel is shown
927 showAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
928 hideAllSeqAnnotations.setEnabled(annotationPanelMenuItem.getState());
929 showAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
930 hideAllAlAnnotations.setEnabled(annotationPanelMenuItem.getState());
931 viewBoxesMenuItem.setSelected(av.getShowBoxes());
932 viewTextMenuItem.setSelected(av.getShowText());
933 showNonconservedMenuItem.setSelected(av.getShowUnconserved());
934 showGroupConsensus.setSelected(av.isShowGroupConsensus());
935 showGroupConservation.setSelected(av.isShowGroupConservation());
936 showConsensusHistogram.setSelected(av.isShowConsensusHistogram());
937 showSequenceLogo.setSelected(av.isShowSequenceLogo());
938 normaliseSequenceLogo.setSelected(av.isNormaliseSequenceLogo());
940 ColourMenuHelper.setColourSelected(colourMenu,
941 av.getGlobalColourScheme());
943 showSeqFeatures.setSelected(av.isShowSequenceFeatures());
944 hiddenMarkers.setState(av.getShowHiddenMarkers());
945 applyToAllGroups.setState(av.getColourAppliesToAllGroups());
946 showNpFeatsMenuitem.setSelected(av.isShowNPFeats());
947 showDbRefsMenuitem.setSelected(av.isShowDBRefs());
948 autoCalculate.setSelected(av.autoCalculateConsensus);
949 sortByTree.setSelected(av.sortByTree);
950 listenToViewSelections.setSelected(av.followSelection);
952 showProducts.setEnabled(canShowProducts());
953 setGroovyEnabled(Desktop.getGroovyConsole() != null);
959 * Set the enabled state of the 'Run Groovy' option in the Calculate menu
963 public void setGroovyEnabled(boolean b)
965 runGroovy.setEnabled(b);
968 private IProgressIndicator progressBar;
973 * @see jalview.gui.IProgressIndicator#setProgressBar(java.lang.String, long)
976 public void setProgressBar(String message, long id)
978 progressBar.setProgressBar(message, id);
982 public void registerHandler(final long id,
983 final IProgressIndicatorHandler handler)
985 progressBar.registerHandler(id, handler);
990 * @return true if any progress bars are still active
993 public boolean operationInProgress()
995 return progressBar.operationInProgress();
999 * Sets the text of the status bar. Note that setting a null or empty value
1000 * will cause the status bar to be hidden, with possibly undesirable flicker
1001 * of the screen layout.
1004 public void setStatus(String text)
1006 statusBar.setText(text == null || text.isEmpty() ? " " : text);
1010 * Added so Castor Mapping file can obtain Jalview Version
1012 public String getVersion()
1014 return jalview.bin.Cache.getProperty("VERSION");
1017 public FeatureRenderer getFeatureRenderer()
1019 return alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer();
1023 public void fetchSequence_actionPerformed()
1025 new SequenceFetcher(this);
1029 public void addFromFile_actionPerformed(ActionEvent e)
1031 Desktop.instance.inputLocalFileMenuItem_actionPerformed(viewport);
1035 public void reload_actionPerformed(ActionEvent e)
1037 if (fileName != null)
1039 // TODO: JAL-1108 - ensure all associated frames are closed regardless of
1040 // originating file's format
1041 // TODO: work out how to recover feature settings for correct view(s) when
1042 // file is reloaded.
1043 if (FileFormat.Jalview.equals(currentFileFormat))
1045 JInternalFrame[] frames = Desktop.desktop.getAllFrames();
1046 for (int i = 0; i < frames.length; i++)
1048 if (frames[i] instanceof AlignFrame && frames[i] != this
1049 && ((AlignFrame) frames[i]).fileName != null
1050 && ((AlignFrame) frames[i]).fileName.equals(fileName))
1054 frames[i].setSelected(true);
1055 Desktop.instance.closeAssociatedWindows();
1056 } catch (java.beans.PropertyVetoException ex)
1062 Desktop.instance.closeAssociatedWindows();
1064 FileLoader loader = new FileLoader();
1065 DataSourceType protocol = fileName.startsWith("http:")
1066 ? DataSourceType.URL
1067 : DataSourceType.FILE;
1068 loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
1072 Rectangle bounds = this.getBounds();
1074 FileLoader loader = new FileLoader();
1076 AlignFrame newframe = null;
1078 if (fileObject == null)
1081 DataSourceType protocol = (fileName.startsWith("http:")
1082 ? DataSourceType.URL
1083 : DataSourceType.FILE);
1084 newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
1089 newframe = loader.LoadFileWaitTillLoaded(fileObject,
1090 DataSourceType.FILE, currentFileFormat);
1093 newframe.setBounds(bounds);
1094 if (featureSettings != null && featureSettings.isShowing())
1096 final Rectangle fspos = featureSettings.frame.getBounds();
1097 // TODO: need a 'show feature settings' function that takes bounds -
1098 // need to refactor Desktop.addFrame
1099 newframe.featureSettings_actionPerformed(null);
1100 final FeatureSettings nfs = newframe.featureSettings;
1101 SwingUtilities.invokeLater(new Runnable()
1106 nfs.frame.setBounds(fspos);
1109 this.featureSettings.close();
1110 this.featureSettings = null;
1112 this.closeMenuItem_actionPerformed(true);
1118 public void addFromText_actionPerformed(ActionEvent e)
1121 .inputTextboxMenuItem_actionPerformed(viewport.getAlignPanel());
1125 public void addFromURL_actionPerformed(ActionEvent e)
1127 Desktop.instance.inputURLMenuItem_actionPerformed(viewport);
1131 public void save_actionPerformed(ActionEvent e)
1133 if (fileName == null || (currentFileFormat == null)
1134 || fileName.startsWith("http"))
1136 saveAs_actionPerformed();
1140 saveAlignment(fileName, currentFileFormat);
1145 * Saves the alignment to a file with a name chosen by the user, if necessary
1146 * warning if a file would be overwritten
1149 public void saveAs_actionPerformed()
1151 String format = currentFileFormat == null ? null
1152 : currentFileFormat.getName();
1153 JalviewFileChooser chooser = JalviewFileChooser
1154 .forWrite(Cache.getProperty("LAST_DIRECTORY"), format);
1156 chooser.setFileView(new JalviewFileView());
1157 chooser.setDialogTitle(
1158 MessageManager.getString("label.save_alignment_to_file"));
1159 chooser.setToolTipText(MessageManager.getString("action.save"));
1161 int value = chooser.showSaveDialog(this);
1163 if (value != JalviewFileChooser.APPROVE_OPTION)
1167 currentFileFormat = chooser.getSelectedFormat();
1168 // todo is this (2005) test now obsolete - value is never null?
1169 while (currentFileFormat == null)
1171 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1173 .getString("label.select_file_format_before_saving"),
1174 MessageManager.getString("label.file_format_not_specified"),
1175 JvOptionPane.WARNING_MESSAGE);
1176 currentFileFormat = chooser.getSelectedFormat();
1177 value = chooser.showSaveDialog(this);
1178 if (value != JalviewFileChooser.APPROVE_OPTION)
1184 fileName = chooser.getSelectedFile().getPath();
1186 Cache.setProperty("DEFAULT_FILE_FORMAT", currentFileFormat.getName());
1187 Cache.setProperty("LAST_DIRECTORY", fileName);
1188 saveAlignment(fileName, currentFileFormat);
1191 boolean lastSaveSuccessful = false;
1193 FileFormatI lastFormatSaved;
1195 String lastFilenameSaved;
1198 * Raise a dialog or status message for the last call to saveAlignment.
1200 * @return true if last call to saveAlignment(file, format) was successful.
1202 public boolean isSaveAlignmentSuccessful()
1205 if (!lastSaveSuccessful)
1207 JvOptionPane.showInternalMessageDialog(this, MessageManager
1208 .formatMessage("label.couldnt_save_file", new Object[]
1209 { lastFilenameSaved }),
1210 MessageManager.getString("label.error_saving_file"),
1211 JvOptionPane.WARNING_MESSAGE);
1216 setStatus(MessageManager.formatMessage(
1217 "label.successfully_saved_to_file_in_format", new Object[]
1218 { lastFilenameSaved, lastFormatSaved }));
1221 return lastSaveSuccessful;
1225 * Saves the alignment to the specified file path, in the specified format,
1226 * which may be an alignment format, or Jalview project format. If the
1227 * alignment has hidden regions, or the format is one capable of including
1228 * non-sequence data (features, annotations, groups), then the user may be
1229 * prompted to specify what to include in the output.
1234 public void saveAlignment(String file, FileFormatI format)
1236 lastSaveSuccessful = true;
1237 lastFilenameSaved = file;
1238 lastFormatSaved = format;
1240 if (FileFormat.Jalview.equals(format))
1242 String shortName = title;
1243 if (shortName.indexOf(File.separatorChar) > -1)
1245 shortName = shortName.substring(
1246 shortName.lastIndexOf(File.separatorChar) + 1);
1248 lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
1250 statusBar.setText(MessageManager.formatMessage(
1251 "label.successfully_saved_to_file_in_format", new Object[]
1252 { fileName, format }));
1257 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1258 Runnable cancelAction = new Runnable()
1263 lastSaveSuccessful = false;
1266 Runnable outputAction = new Runnable()
1271 // todo defer this to inside formatSequences (or later)
1272 AlignmentExportData exportData = viewport
1273 .getAlignExportData(options);
1274 String output = new FormatAdapter(alignPanel, options)
1275 .formatSequences(format, exportData.getAlignment(),
1276 exportData.getOmitHidden(),
1277 exportData.getStartEndPostions(),
1278 viewport.getAlignment().getHiddenColumns());
1281 lastSaveSuccessful = false;
1285 // create backupfiles object and get new temp filename destination
1286 boolean doBackup = BackupFiles.getEnabled();
1287 BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
1290 String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
1291 PrintWriter out = new PrintWriter(
1292 new FileWriter(tempFilePath));
1296 AlignFrame.this.setTitle(file);
1297 statusBar.setText(MessageManager.formatMessage(
1298 "label.successfully_saved_to_file_in_format", new Object[]
1299 { fileName, format.getName() }));
1300 lastSaveSuccessful = true;
1301 } catch (Exception ex)
1303 lastSaveSuccessful = false;
1304 ex.printStackTrace();
1309 backupfiles.setWriteSuccess(lastSaveSuccessful);
1310 // do the backup file roll and rename the temp file to actual file
1311 lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
1318 * show dialog with export options if applicable; else just do it
1320 if (AlignExportOptions.isNeeded(viewport, format))
1322 AlignExportOptions choices = new AlignExportOptions(
1323 alignPanel.getAlignViewport(), format, options);
1324 choices.setResponseAction(0, outputAction);
1325 choices.setResponseAction(1, cancelAction);
1326 choices.showDialog();
1335 * Outputs the alignment to textbox in the requested format, if necessary
1336 * first prompting the user for whether to include hidden regions or
1339 * @param fileFormatName
1342 protected void outputText_actionPerformed(String fileFormatName)
1344 FileFormatI fileFormat = FileFormats.getInstance()
1345 .forName(fileFormatName);
1346 AlignExportSettingsI options = new AlignExportSettingsAdapter(false);
1347 Runnable outputAction = new Runnable()
1352 // todo defer this to inside formatSequences (or later)
1353 AlignmentExportData exportData = viewport
1354 .getAlignExportData(options);
1355 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1356 cap.setForInput(null);
1359 FileFormatI format = fileFormat;
1360 cap.setText(new FormatAdapter(alignPanel, options)
1361 .formatSequences(format, exportData.getAlignment(),
1362 exportData.getOmitHidden(),
1363 exportData.getStartEndPostions(),
1364 viewport.getAlignment().getHiddenColumns()));
1365 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1366 "label.alignment_output_command", new Object[]
1367 { fileFormat.getName() }), 600, 500);
1368 } catch (OutOfMemoryError oom)
1370 new OOMWarning("Outputting alignment as " + fileFormat.getName(),
1378 * show dialog with export options if applicable; else just do it
1380 if (AlignExportOptions.isNeeded(viewport, fileFormat))
1382 AlignExportOptions choices = new AlignExportOptions(
1383 alignPanel.getAlignViewport(), fileFormat, options);
1384 choices.setResponseAction(0, outputAction);
1385 choices.showDialog();
1400 protected void htmlMenuItem_actionPerformed(ActionEvent e)
1402 HtmlSvgOutput htmlSVG = new HtmlSvgOutput(alignPanel);
1403 htmlSVG.exportHTML(null);
1407 public void bioJSMenuItem_actionPerformed(ActionEvent e)
1409 BioJsHTMLOutput bjs = new BioJsHTMLOutput(alignPanel);
1410 bjs.exportHTML(null);
1413 public void createImageMap(File file, String image)
1415 alignPanel.makePNGImageMap(file, image);
1419 * Creates a PNG image of the alignment and writes it to the given file. If
1420 * the file is null, the user is prompted to choose a file.
1425 public void createPNG(File f)
1427 alignPanel.makeAlignmentImage(TYPE.PNG, f);
1431 * Creates an EPS image of the alignment and writes it to the given file. If
1432 * the file is null, the user is prompted to choose a file.
1437 public void createEPS(File f)
1439 alignPanel.makeAlignmentImage(TYPE.EPS, f);
1443 * Creates an SVG image of the alignment and writes it to the given file. If
1444 * the file is null, the user is prompted to choose a file.
1449 public void createSVG(File f)
1451 alignPanel.makeAlignmentImage(TYPE.SVG, f);
1455 public void pageSetup_actionPerformed(ActionEvent e)
1457 PrinterJob printJob = PrinterJob.getPrinterJob();
1458 PrintThread.pf = printJob.pageDialog(printJob.defaultPage());
1468 public void printMenuItem_actionPerformed(ActionEvent e)
1470 // Putting in a thread avoids Swing painting problems
1471 PrintThread thread = new PrintThread(alignPanel);
1476 public void exportFeatures_actionPerformed(ActionEvent e)
1478 new AnnotationExporter(alignPanel).exportFeatures();
1482 public void exportAnnotations_actionPerformed(ActionEvent e)
1484 new AnnotationExporter(alignPanel).exportAnnotations();
1488 public void associatedData_actionPerformed(ActionEvent e)
1490 final JalviewFileChooser chooser = new JalviewFileChooser(
1491 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1492 chooser.setFileView(new JalviewFileView());
1493 chooser.setDialogTitle(
1494 MessageManager.getString("label.load_jalview_annotations"));
1495 chooser.setToolTipText(
1496 MessageManager.getString("label.load_jalview_annotations"));
1497 chooser.setResponseHandler(0, new Runnable()
1502 String choice = chooser.getSelectedFile().getPath();
1503 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1504 loadJalviewDataFile(chooser.getSelectedFile(), null, null, null);
1508 chooser.showOpenDialog(this);
1512 * Close the current view or all views in the alignment frame. If the frame
1513 * only contains one view then the alignment will be removed from memory.
1515 * @param closeAllTabs
1518 public void closeMenuItem_actionPerformed(boolean closeAllTabs)
1520 if (alignPanels != null && alignPanels.size() < 2)
1522 closeAllTabs = true;
1527 if (alignPanels != null)
1531 if (this.isClosed())
1533 // really close all the windows - otherwise wait till
1534 // setClosed(true) is called
1535 for (int i = 0; i < alignPanels.size(); i++)
1537 AlignmentPanel ap = alignPanels.get(i);
1544 closeView(alignPanel);
1551 * this will raise an INTERNAL_FRAME_CLOSED event and this method will
1552 * be called recursively, with the frame now in 'closed' state
1554 this.setClosed(true);
1556 } catch (Exception ex)
1558 ex.printStackTrace();
1563 * Close the specified panel and close up tabs appropriately.
1565 * @param panelToClose
1567 public void closeView(AlignmentPanel panelToClose)
1569 int index = tabbedPane.getSelectedIndex();
1570 int closedindex = tabbedPane.indexOfComponent(panelToClose);
1571 alignPanels.remove(panelToClose);
1572 panelToClose.closePanel();
1573 panelToClose = null;
1575 tabbedPane.removeTabAt(closedindex);
1576 tabbedPane.validate();
1578 if (index > closedindex || index == tabbedPane.getTabCount())
1580 // modify currently selected tab index if necessary.
1584 this.tabSelectionChanged(index);
1590 void updateEditMenuBar()
1593 if (viewport.getHistoryList().size() > 0)
1595 undoMenuItem.setEnabled(true);
1596 CommandI command = viewport.getHistoryList().peek();
1597 undoMenuItem.setText(MessageManager
1598 .formatMessage("label.undo_command", new Object[]
1599 { command.getDescription() }));
1603 undoMenuItem.setEnabled(false);
1604 undoMenuItem.setText(MessageManager.getString("action.undo"));
1607 if (viewport.getRedoList().size() > 0)
1609 redoMenuItem.setEnabled(true);
1611 CommandI command = viewport.getRedoList().peek();
1612 redoMenuItem.setText(MessageManager
1613 .formatMessage("label.redo_command", new Object[]
1614 { command.getDescription() }));
1618 redoMenuItem.setEnabled(false);
1619 redoMenuItem.setText(MessageManager.getString("action.redo"));
1624 public void addHistoryItem(CommandI command)
1626 if (command.getSize() > 0)
1628 viewport.addToHistoryList(command);
1629 viewport.clearRedoList();
1630 updateEditMenuBar();
1631 viewport.updateHiddenColumns();
1632 // viewport.hasHiddenColumns = (viewport.getColumnSelection() != null
1633 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1634 // viewport.getColumnSelection()
1635 // .getHiddenColumns().size() > 0);
1641 * @return alignment objects for all views
1643 AlignmentI[] getViewAlignments()
1645 if (alignPanels != null)
1647 AlignmentI[] als = new AlignmentI[alignPanels.size()];
1649 for (AlignmentPanel ap : alignPanels)
1651 als[i++] = ap.av.getAlignment();
1655 if (viewport != null)
1657 return new AlignmentI[] { viewport.getAlignment() };
1669 protected void undoMenuItem_actionPerformed(ActionEvent e)
1671 if (viewport.getHistoryList().isEmpty())
1675 CommandI command = viewport.getHistoryList().pop();
1676 viewport.addToRedoList(command);
1677 command.undoCommand(getViewAlignments());
1679 AlignmentViewport originalSource = getOriginatingSource(command);
1680 updateEditMenuBar();
1682 if (originalSource != null)
1684 if (originalSource != viewport)
1687 "Implementation worry: mismatch of viewport origin for undo");
1689 originalSource.updateHiddenColumns();
1690 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1692 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1693 // viewport.getColumnSelection()
1694 // .getHiddenColumns().size() > 0);
1695 originalSource.firePropertyChange("alignment", null,
1696 originalSource.getAlignment().getSequences());
1707 protected void redoMenuItem_actionPerformed(ActionEvent e)
1709 if (viewport.getRedoList().size() < 1)
1714 CommandI command = viewport.getRedoList().pop();
1715 viewport.addToHistoryList(command);
1716 command.doCommand(getViewAlignments());
1718 AlignmentViewport originalSource = getOriginatingSource(command);
1719 updateEditMenuBar();
1721 if (originalSource != null)
1724 if (originalSource != viewport)
1727 "Implementation worry: mismatch of viewport origin for redo");
1729 originalSource.updateHiddenColumns();
1730 // originalSource.hasHiddenColumns = (viewport.getColumnSelection() !=
1732 // && viewport.getColumnSelection().getHiddenColumns() != null &&
1733 // viewport.getColumnSelection()
1734 // .getHiddenColumns().size() > 0);
1735 originalSource.firePropertyChange("alignment", null,
1736 originalSource.getAlignment().getSequences());
1740 AlignmentViewport getOriginatingSource(CommandI command)
1742 AlignmentViewport originalSource = null;
1743 // For sequence removal and addition, we need to fire
1744 // the property change event FROM the viewport where the
1745 // original alignment was altered
1746 AlignmentI al = null;
1747 if (command instanceof EditCommand)
1749 EditCommand editCommand = (EditCommand) command;
1750 al = editCommand.getAlignment();
1751 List<Component> comps = PaintRefresher.components
1752 .get(viewport.getSequenceSetId());
1754 for (Component comp : comps)
1756 if (comp instanceof AlignmentPanel)
1758 if (al == ((AlignmentPanel) comp).av.getAlignment())
1760 originalSource = ((AlignmentPanel) comp).av;
1767 if (originalSource == null)
1769 // The original view is closed, we must validate
1770 // the current view against the closed view first
1773 PaintRefresher.validateSequences(al, viewport.getAlignment());
1776 originalSource = viewport;
1779 return originalSource;
1788 public void moveSelectedSequences(boolean up)
1790 SequenceGroup sg = viewport.getSelectionGroup();
1796 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1797 viewport.getHiddenRepSequences(), up);
1798 alignPanel.paintAlignment(true, false);
1801 synchronized void slideSequences(boolean right, int size)
1803 List<SequenceI> sg = new ArrayList<>();
1804 if (viewport.cursorMode)
1806 sg.add(viewport.getAlignment()
1807 .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY));
1809 else if (viewport.getSelectionGroup() != null
1810 && viewport.getSelectionGroup().getSize() != viewport
1811 .getAlignment().getHeight())
1813 sg = viewport.getSelectionGroup()
1814 .getSequences(viewport.getHiddenRepSequences());
1822 List<SequenceI> invertGroup = new ArrayList<>();
1824 for (SequenceI seq : viewport.getAlignment().getSequences())
1826 if (!sg.contains(seq))
1828 invertGroup.add(seq);
1832 SequenceI[] seqs1 = sg.toArray(new SequenceI[0]);
1834 SequenceI[] seqs2 = new SequenceI[invertGroup.size()];
1835 for (int i = 0; i < invertGroup.size(); i++)
1837 seqs2[i] = invertGroup.get(i);
1840 SlideSequencesCommand ssc;
1843 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1, size,
1844 viewport.getGapCharacter());
1848 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2, size,
1849 viewport.getGapCharacter());
1852 int groupAdjustment = 0;
1853 if (ssc.getGapsInsertedBegin() && right)
1855 if (viewport.cursorMode)
1857 alignPanel.getSeqPanel().moveCursor(size, 0);
1861 groupAdjustment = size;
1864 else if (!ssc.getGapsInsertedBegin() && !right)
1866 if (viewport.cursorMode)
1868 alignPanel.getSeqPanel().moveCursor(-size, 0);
1872 groupAdjustment = -size;
1876 if (groupAdjustment != 0)
1878 viewport.getSelectionGroup().setStartRes(
1879 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1880 viewport.getSelectionGroup().setEndRes(
1881 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1885 * just extend the last slide command if compatible; but not if in
1886 * SplitFrame mode (to ensure all edits are broadcast - JAL-1802)
1888 boolean appendHistoryItem = false;
1889 Deque<CommandI> historyList = viewport.getHistoryList();
1890 boolean inSplitFrame = getSplitViewContainer() != null;
1891 if (!inSplitFrame && historyList != null && historyList.size() > 0
1892 && historyList.peek() instanceof SlideSequencesCommand)
1894 appendHistoryItem = ssc.appendSlideCommand(
1895 (SlideSequencesCommand) historyList.peek());
1898 if (!appendHistoryItem)
1900 addHistoryItem(ssc);
1913 protected void copy_actionPerformed()
1915 if (viewport.getSelectionGroup() == null)
1919 // TODO: preserve the ordering of displayed alignment annotation in any
1920 // internal paste (particularly sequence associated annotation)
1921 SequenceI[] seqs = viewport.getSelectionAsNewSequence();
1922 String[] omitHidden = null;
1924 if (viewport.hasHiddenColumns())
1926 omitHidden = viewport.getViewAsString(true);
1929 String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
1930 seqs, omitHidden, null);
1932 StringSelection ss = new StringSelection(output);
1936 jalview.gui.Desktop.internalCopy = true;
1937 // Its really worth setting the clipboard contents
1938 // to empty before setting the large StringSelection!!
1939 Toolkit.getDefaultToolkit().getSystemClipboard()
1940 .setContents(new StringSelection(""), null);
1942 Toolkit.getDefaultToolkit().getSystemClipboard().setContents(ss,
1944 } catch (OutOfMemoryError er)
1946 new OOMWarning("copying region", er);
1950 HiddenColumns hiddenColumns = null;
1951 if (viewport.hasHiddenColumns())
1953 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1954 int hiddenCutoff = viewport.getSelectionGroup().getEndRes();
1956 // create new HiddenColumns object with copy of hidden regions
1957 // between startRes and endRes, offset by startRes
1958 hiddenColumns = new HiddenColumns(
1959 viewport.getAlignment().getHiddenColumns(), hiddenOffset,
1960 hiddenCutoff, hiddenOffset);
1963 Desktop.jalviewClipboard = new Object[] { seqs,
1964 viewport.getAlignment().getDataset(), hiddenColumns };
1965 setStatus(MessageManager.formatMessage(
1966 "label.copied_sequences_to_clipboard", new Object[]
1967 { Integer.valueOf(seqs.length).toString() }));
1977 protected void pasteNew_actionPerformed(ActionEvent e)
1989 protected void pasteThis_actionPerformed(ActionEvent e)
1995 * Paste contents of Jalview clipboard
1997 * @param newAlignment
1998 * true to paste to a new alignment, otherwise add to this.
2000 void paste(boolean newAlignment)
2002 boolean externalPaste = true;
2005 Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard();
2006 Transferable contents = c.getContents(this);
2008 if (contents == null)
2017 str = (String) contents.getTransferData(DataFlavor.stringFlavor);
2018 if (str.length() < 1)
2023 format = new IdentifyFile().identify(str, DataSourceType.PASTE);
2025 } catch (OutOfMemoryError er)
2027 new OOMWarning("Out of memory pasting sequences!!", er);
2031 SequenceI[] sequences;
2032 boolean annotationAdded = false;
2033 AlignmentI alignment = null;
2035 if (Desktop.jalviewClipboard != null)
2037 // The clipboard was filled from within Jalview, we must use the
2039 // And dataset from the copied alignment
2040 SequenceI[] newseq = (SequenceI[]) Desktop.jalviewClipboard[0];
2041 // be doubly sure that we create *new* sequence objects.
2042 sequences = new SequenceI[newseq.length];
2043 for (int i = 0; i < newseq.length; i++)
2045 sequences[i] = new Sequence(newseq[i]);
2047 alignment = new Alignment(sequences);
2048 externalPaste = false;
2052 // parse the clipboard as an alignment.
2053 alignment = new FormatAdapter().readFile(str, DataSourceType.PASTE,
2055 sequences = alignment.getSequencesArray();
2059 ArrayList<Integer> newGraphGroups = new ArrayList<>();
2065 if (Desktop.jalviewClipboard != null)
2067 // dataset is inherited
2068 alignment.setDataset((Alignment) Desktop.jalviewClipboard[1]);
2072 // new dataset is constructed
2073 alignment.setDataset(null);
2075 alwidth = alignment.getWidth() + 1;
2079 AlignmentI pastedal = alignment; // preserve pasted alignment object
2080 // Add pasted sequences and dataset into existing alignment.
2081 alignment = viewport.getAlignment();
2082 alwidth = alignment.getWidth() + 1;
2083 // decide if we need to import sequences from an existing dataset
2084 boolean importDs = Desktop.jalviewClipboard != null
2085 && Desktop.jalviewClipboard[1] != alignment.getDataset();
2086 // importDs==true instructs us to copy over new dataset sequences from
2087 // an existing alignment
2088 Vector<SequenceI> newDs = (importDs) ? new Vector<>() : null; // used to
2090 // minimum dataset set
2092 for (int i = 0; i < sequences.length; i++)
2096 newDs.addElement(null);
2098 SequenceI ds = sequences[i].getDatasetSequence(); // null for a simple
2100 if (importDs && ds != null)
2102 if (!newDs.contains(ds))
2104 newDs.setElementAt(ds, i);
2105 ds = new Sequence(ds);
2106 // update with new dataset sequence
2107 sequences[i].setDatasetSequence(ds);
2111 ds = sequences[newDs.indexOf(ds)].getDatasetSequence();
2116 // copy and derive new dataset sequence
2117 sequences[i] = sequences[i].deriveSequence();
2118 alignment.getDataset()
2119 .addSequence(sequences[i].getDatasetSequence());
2120 // TODO: avoid creation of duplicate dataset sequences with a
2121 // 'contains' method using SequenceI.equals()/SequenceI.contains()
2123 alignment.addSequence(sequences[i]); // merges dataset
2127 newDs.clear(); // tidy up
2129 if (alignment.getAlignmentAnnotation() != null)
2131 for (AlignmentAnnotation alan : alignment
2132 .getAlignmentAnnotation())
2134 if (alan.graphGroup > fgroup)
2136 fgroup = alan.graphGroup;
2140 if (pastedal.getAlignmentAnnotation() != null)
2142 // Add any annotation attached to alignment.
2143 AlignmentAnnotation[] alann = pastedal.getAlignmentAnnotation();
2144 for (int i = 0; i < alann.length; i++)
2146 annotationAdded = true;
2147 if (alann[i].sequenceRef == null && !alann[i].autoCalculated)
2149 AlignmentAnnotation newann = new AlignmentAnnotation(
2151 if (newann.graphGroup > -1)
2153 if (newGraphGroups.size() <= newann.graphGroup
2154 || newGraphGroups.get(newann.graphGroup) == null)
2156 for (int q = newGraphGroups
2157 .size(); q <= newann.graphGroup; q++)
2159 newGraphGroups.add(q, null);
2161 newGraphGroups.set(newann.graphGroup,
2162 Integer.valueOf(++fgroup));
2164 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2168 newann.padAnnotation(alwidth);
2169 alignment.addAnnotation(newann);
2179 addHistoryItem(new EditCommand(
2180 MessageManager.getString("label.add_sequences"),
2181 Action.PASTE, sequences, 0, alignment.getWidth(),
2184 // Add any annotations attached to sequences
2185 for (int i = 0; i < sequences.length; i++)
2187 if (sequences[i].getAnnotation() != null)
2189 AlignmentAnnotation newann;
2190 for (int a = 0; a < sequences[i].getAnnotation().length; a++)
2192 annotationAdded = true;
2193 newann = sequences[i].getAnnotation()[a];
2194 newann.adjustForAlignment();
2195 newann.padAnnotation(alwidth);
2196 if (newann.graphGroup > -1)
2198 if (newann.graphGroup > -1)
2200 if (newGraphGroups.size() <= newann.graphGroup
2201 || newGraphGroups.get(newann.graphGroup) == null)
2203 for (int q = newGraphGroups
2204 .size(); q <= newann.graphGroup; q++)
2206 newGraphGroups.add(q, null);
2208 newGraphGroups.set(newann.graphGroup,
2209 Integer.valueOf(++fgroup));
2211 newann.graphGroup = newGraphGroups.get(newann.graphGroup)
2215 alignment.addAnnotation(sequences[i].getAnnotation()[a]); // annotation
2219 alignment.setAnnotationIndex(sequences[i].getAnnotation()[a],
2227 // propagate alignment changed.
2228 viewport.getRanges().setEndSeq(alignment.getHeight() - 1);
2229 if (annotationAdded)
2231 // Duplicate sequence annotation in all views.
2232 AlignmentI[] alview = this.getViewAlignments();
2233 for (int i = 0; i < sequences.length; i++)
2235 AlignmentAnnotation sann[] = sequences[i].getAnnotation();
2240 for (int avnum = 0; avnum < alview.length; avnum++)
2242 if (alview[avnum] != alignment)
2244 // duplicate in a view other than the one with input focus
2245 int avwidth = alview[avnum].getWidth() + 1;
2246 // this relies on sann being preserved after we
2247 // modify the sequence's annotation array for each duplication
2248 for (int a = 0; a < sann.length; a++)
2250 AlignmentAnnotation newann = new AlignmentAnnotation(
2252 sequences[i].addAlignmentAnnotation(newann);
2253 newann.padAnnotation(avwidth);
2254 alview[avnum].addAnnotation(newann); // annotation was
2255 // duplicated earlier
2256 // TODO JAL-1145 graphGroups are not updated for sequence
2257 // annotation added to several views. This may cause
2259 alview[avnum].setAnnotationIndex(newann, a);
2264 buildSortByAnnotationScoresMenu();
2266 viewport.firePropertyChange("alignment", null,
2267 alignment.getSequences());
2268 if (alignPanels != null)
2270 for (AlignmentPanel ap : alignPanels)
2272 ap.validateAnnotationDimensions(false);
2277 alignPanel.validateAnnotationDimensions(false);
2283 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2285 String newtitle = new String("Copied sequences");
2287 if (Desktop.jalviewClipboard != null
2288 && Desktop.jalviewClipboard[2] != null)
2290 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2291 af.viewport.setHiddenColumns(hc);
2294 // >>>This is a fix for the moment, until a better solution is
2296 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2297 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2298 .getFeatureRenderer());
2300 // TODO: maintain provenance of an alignment, rather than just make the
2301 // title a concatenation of operations.
2304 if (title.startsWith("Copied sequences"))
2310 newtitle = newtitle.concat("- from " + title);
2315 newtitle = new String("Pasted sequences");
2318 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH,
2323 } catch (Exception ex)
2325 ex.printStackTrace();
2326 System.out.println("Exception whilst pasting: " + ex);
2327 // could be anything being pasted in here
2333 protected void expand_newalign(ActionEvent e)
2337 AlignmentI alignment = AlignmentUtils
2338 .expandContext(getViewport().getAlignment(), -1);
2339 AlignFrame af = new AlignFrame(alignment, DEFAULT_WIDTH,
2341 String newtitle = new String("Flanking alignment");
2343 if (Desktop.jalviewClipboard != null
2344 && Desktop.jalviewClipboard[2] != null)
2346 HiddenColumns hc = (HiddenColumns) Desktop.jalviewClipboard[2];
2347 af.viewport.setHiddenColumns(hc);
2350 // >>>This is a fix for the moment, until a better solution is
2352 af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
2353 .transferSettings(alignPanel.getSeqPanel().seqCanvas
2354 .getFeatureRenderer());
2356 // TODO: maintain provenance of an alignment, rather than just make the
2357 // title a concatenation of operations.
2359 if (title.startsWith("Copied sequences"))
2365 newtitle = newtitle.concat("- from " + title);
2369 Desktop.addInternalFrame(af, newtitle, DEFAULT_WIDTH, DEFAULT_HEIGHT);
2371 } catch (Exception ex)
2373 ex.printStackTrace();
2374 System.out.println("Exception whilst pasting: " + ex);
2375 // could be anything being pasted in here
2376 } catch (OutOfMemoryError oom)
2378 new OOMWarning("Viewing flanking region of alignment", oom);
2383 * Action Cut (delete and copy) the selected region
2386 protected void cut_actionPerformed()
2388 copy_actionPerformed();
2389 delete_actionPerformed();
2393 * Performs menu option to Delete the currently selected region
2396 protected void delete_actionPerformed()
2399 SequenceGroup sg = viewport.getSelectionGroup();
2405 Runnable okAction = new Runnable()
2410 SequenceI[] cut = sg.getSequences()
2411 .toArray(new SequenceI[sg.getSize()]);
2413 addHistoryItem(new EditCommand(
2414 MessageManager.getString("label.cut_sequences"), Action.CUT,
2415 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2416 viewport.getAlignment()));
2418 viewport.setSelectionGroup(null);
2419 viewport.sendSelection();
2420 viewport.getAlignment().deleteGroup(sg);
2422 viewport.firePropertyChange("alignment", null,
2423 viewport.getAlignment().getSequences());
2424 if (viewport.getAlignment().getHeight() < 1)
2428 AlignFrame.this.setClosed(true);
2429 } catch (Exception ex)
2436 * If the cut affects all sequences, prompt for confirmation
2438 boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
2439 boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
2440 + 1) == viewport.getAlignment().getWidth()) ? true : false;
2441 if (wholeHeight && wholeWidth)
2443 JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
2444 dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
2445 Object[] options = new Object[] { MessageManager.getString("action.ok"),
2446 MessageManager.getString("action.cancel") };
2447 dialog.showDialog(MessageManager.getString("warn.delete_all"),
2448 MessageManager.getString("label.delete_all"),
2449 JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
2450 options, options[0]);
2464 protected void deleteGroups_actionPerformed(ActionEvent e)
2466 if (avc.deleteGroups())
2468 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2469 alignPanel.updateAnnotation();
2470 alignPanel.paintAlignment(true, true);
2481 public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2483 SequenceGroup sg = new SequenceGroup(
2484 viewport.getAlignment().getSequences());
2486 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2487 viewport.setSelectionGroup(sg);
2488 viewport.isSelectionGroupChanged(true);
2489 viewport.sendSelection();
2490 // JAL-2034 - should delegate to
2491 // alignPanel to decide if overview needs
2493 alignPanel.paintAlignment(false, false);
2494 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2504 public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)
2506 if (viewport.cursorMode)
2508 alignPanel.getSeqPanel().keyboardNo1 = null;
2509 alignPanel.getSeqPanel().keyboardNo2 = null;
2511 viewport.setSelectionGroup(null);
2512 viewport.getColumnSelection().clear();
2513 viewport.setSelectionGroup(null);
2514 alignPanel.getIdPanel().getIdCanvas().searchResults = null;
2515 // JAL-2034 - should delegate to
2516 // alignPanel to decide if overview needs
2518 alignPanel.paintAlignment(false, false);
2519 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2520 viewport.sendSelection();
2530 public void invertSequenceMenuItem_actionPerformed(ActionEvent e)
2532 SequenceGroup sg = viewport.getSelectionGroup();
2536 selectAllSequenceMenuItem_actionPerformed(null);
2541 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2543 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2545 // JAL-2034 - should delegate to
2546 // alignPanel to decide if overview needs
2549 alignPanel.paintAlignment(true, false);
2550 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2551 viewport.sendSelection();
2555 public void invertColSel_actionPerformed(ActionEvent e)
2557 viewport.invertColumnSelection();
2558 alignPanel.paintAlignment(true, false);
2559 viewport.sendSelection();
2569 public void remove2LeftMenuItem_actionPerformed(ActionEvent e)
2571 trimAlignment(true);
2581 public void remove2RightMenuItem_actionPerformed(ActionEvent e)
2583 trimAlignment(false);
2586 void trimAlignment(boolean trimLeft)
2588 ColumnSelection colSel = viewport.getColumnSelection();
2591 if (!colSel.isEmpty())
2595 column = colSel.getMin();
2599 column = colSel.getMax();
2603 if (viewport.getSelectionGroup() != null)
2605 seqs = viewport.getSelectionGroup()
2606 .getSequencesAsArray(viewport.getHiddenRepSequences());
2610 seqs = viewport.getAlignment().getSequencesArray();
2613 TrimRegionCommand trimRegion;
2616 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2617 column, viewport.getAlignment());
2618 viewport.getRanges().setStartRes(0);
2622 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2623 column, viewport.getAlignment());
2626 setStatus(MessageManager
2627 .formatMessage("label.removed_columns", new String[]
2628 { Integer.valueOf(trimRegion.getSize()).toString() }));
2630 addHistoryItem(trimRegion);
2632 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2634 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2635 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2637 viewport.getAlignment().deleteGroup(sg);
2641 viewport.firePropertyChange("alignment", null,
2642 viewport.getAlignment().getSequences());
2653 public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)
2655 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2658 if (viewport.getSelectionGroup() != null)
2660 seqs = viewport.getSelectionGroup()
2661 .getSequencesAsArray(viewport.getHiddenRepSequences());
2662 start = viewport.getSelectionGroup().getStartRes();
2663 end = viewport.getSelectionGroup().getEndRes();
2667 seqs = viewport.getAlignment().getSequencesArray();
2670 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2671 "Remove Gapped Columns", seqs, start, end,
2672 viewport.getAlignment());
2674 addHistoryItem(removeGapCols);
2676 setStatus(MessageManager
2677 .formatMessage("label.removed_empty_columns", new Object[]
2678 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2680 // This is to maintain viewport position on first residue
2681 // of first sequence
2682 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2683 ViewportRanges ranges = viewport.getRanges();
2684 int startRes = seq.findPosition(ranges.getStartRes());
2685 // ShiftList shifts;
2686 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2687 // edit.alColumnChanges=shifts.getInverse();
2688 // if (viewport.hasHiddenColumns)
2689 // viewport.getColumnSelection().compensateForEdits(shifts);
2690 ranges.setStartRes(seq.findIndex(startRes) - 1);
2691 viewport.firePropertyChange("alignment", null,
2692 viewport.getAlignment().getSequences());
2703 public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)
2705 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2708 if (viewport.getSelectionGroup() != null)
2710 seqs = viewport.getSelectionGroup()
2711 .getSequencesAsArray(viewport.getHiddenRepSequences());
2712 start = viewport.getSelectionGroup().getStartRes();
2713 end = viewport.getSelectionGroup().getEndRes();
2717 seqs = viewport.getAlignment().getSequencesArray();
2720 // This is to maintain viewport position on first residue
2721 // of first sequence
2722 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2723 int startRes = seq.findPosition(viewport.getRanges().getStartRes());
2725 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2726 viewport.getAlignment()));
2728 viewport.getRanges().setStartRes(seq.findIndex(startRes) - 1);
2730 viewport.firePropertyChange("alignment", null,
2731 viewport.getAlignment().getSequences());
2742 public void padGapsMenuitem_actionPerformed(ActionEvent e)
2744 viewport.setPadGaps(padGapsMenuitem.isSelected());
2745 viewport.firePropertyChange("alignment", null,
2746 viewport.getAlignment().getSequences());
2756 public void findMenuItem_actionPerformed(ActionEvent e)
2762 * Create a new view of the current alignment.
2765 public void newView_actionPerformed(ActionEvent e)
2767 newView(null, true);
2771 * Creates and shows a new view of the current alignment.
2774 * title of newly created view; if null, one will be generated
2775 * @param copyAnnotation
2776 * if true then duplicate all annnotation, groups and settings
2777 * @return new alignment panel, already displayed.
2779 public AlignmentPanel newView(String viewTitle, boolean copyAnnotation)
2782 * Create a new AlignmentPanel (with its own, new Viewport)
2784 AlignmentPanel newap = new jalview.project.Jalview2XML()
2785 .copyAlignPanel(alignPanel);
2786 if (!copyAnnotation)
2789 * remove all groups and annotation except for the automatic stuff
2791 newap.av.getAlignment().deleteAllGroups();
2792 newap.av.getAlignment().deleteAllAnnotations(false);
2795 newap.av.setGatherViewsHere(false);
2797 if (viewport.getViewName() == null)
2799 viewport.setViewName(MessageManager
2800 .getString("label.view_name_original"));
2804 * Views share the same edits undo and redo stacks
2806 newap.av.setHistoryList(viewport.getHistoryList());
2807 newap.av.setRedoList(viewport.getRedoList());
2810 * copy any visualisation settings that are not saved in the project
2812 newap.av.setColourAppliesToAllGroups(
2813 viewport.getColourAppliesToAllGroups());
2816 * Views share the same mappings; need to deregister any new mappings
2817 * created by copyAlignPanel, and register the new reference to the shared
2820 newap.av.replaceMappings(viewport.getAlignment());
2823 * start up cDNA consensus (if applicable) now mappings are in place
2825 if (newap.av.initComplementConsensus())
2827 newap.refresh(true); // adjust layout of annotations
2830 newap.av.setViewName(getNewViewName(viewTitle));
2832 addAlignmentPanel(newap, true);
2833 newap.alignmentChanged();
2835 if (alignPanels.size() == 2)
2837 viewport.setGatherViewsHere(true);
2839 tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
2844 * Make a new name for the view, ensuring it is unique within the current
2845 * sequenceSetId. (This used to be essential for Jalview Project archives, but
2846 * these now use viewId. Unique view names are still desirable for usability.)
2851 protected String getNewViewName(String viewTitle)
2853 int index = Desktop.getViewCount(viewport.getSequenceSetId());
2854 boolean addFirstIndex = false;
2855 if (viewTitle == null || viewTitle.trim().length() == 0)
2857 viewTitle = MessageManager.getString("action.view");
2858 addFirstIndex = true;
2862 index = 1;// we count from 1 if given a specific name
2864 String newViewName = viewTitle + ((addFirstIndex) ? " " + index : "");
2866 List<Component> comps = PaintRefresher.components
2867 .get(viewport.getSequenceSetId());
2869 List<String> existingNames = getExistingViewNames(comps);
2871 while (existingNames.contains(newViewName))
2873 newViewName = viewTitle + " " + (++index);
2879 * Returns a list of distinct view names found in the given list of
2880 * components. View names are held on the viewport of an AlignmentPanel.
2885 protected List<String> getExistingViewNames(List<Component> comps)
2887 List<String> existingNames = new ArrayList<>();
2888 for (Component comp : comps)
2890 if (comp instanceof AlignmentPanel)
2892 AlignmentPanel ap = (AlignmentPanel) comp;
2893 if (!existingNames.contains(ap.av.getViewName()))
2895 existingNames.add(ap.av.getViewName());
2899 return existingNames;
2903 * Explode tabbed views into separate windows.
2906 public void expandViews_actionPerformed(ActionEvent e)
2908 Desktop.explodeViews(this);
2912 * Gather views in separate windows back into a tabbed presentation.
2915 public void gatherViews_actionPerformed(ActionEvent e)
2917 Desktop.instance.gatherViews(this);
2927 public void font_actionPerformed(ActionEvent e)
2929 new FontChooser(alignPanel);
2939 protected void seqLimit_actionPerformed(ActionEvent e)
2941 viewport.setShowJVSuffix(seqLimits.isSelected());
2943 alignPanel.getIdPanel().getIdCanvas()
2944 .setPreferredSize(alignPanel.calculateIdWidth());
2945 alignPanel.paintAlignment(true, false);
2949 public void idRightAlign_actionPerformed(ActionEvent e)
2951 viewport.setRightAlignIds(idRightAlign.isSelected());
2952 alignPanel.paintAlignment(false, false);
2956 public void centreColumnLabels_actionPerformed(ActionEvent e)
2958 viewport.setCentreColumnLabels(centreColumnLabelsMenuItem.getState());
2959 alignPanel.paintAlignment(false, false);
2965 * @see jalview.jbgui.GAlignFrame#followHighlight_actionPerformed()
2968 protected void followHighlight_actionPerformed()
2971 * Set the 'follow' flag on the Viewport (and scroll to position if now
2974 final boolean state = this.followHighlightMenuItem.getState();
2975 viewport.setFollowHighlight(state);
2978 alignPanel.scrollToPosition(viewport.getSearchResults());
2989 protected void colourTextMenuItem_actionPerformed(ActionEvent e)
2991 viewport.setColourText(colourTextMenuItem.isSelected());
2992 alignPanel.paintAlignment(false, false);
3002 public void wrapMenuItem_actionPerformed(ActionEvent e)
3004 scaleAbove.setVisible(wrapMenuItem.isSelected());
3005 scaleLeft.setVisible(wrapMenuItem.isSelected());
3006 scaleRight.setVisible(wrapMenuItem.isSelected());
3007 viewport.setWrapAlignment(wrapMenuItem.isSelected());
3008 alignPanel.updateLayout();
3012 public void showAllSeqs_actionPerformed(ActionEvent e)
3014 viewport.showAllHiddenSeqs();
3018 public void showAllColumns_actionPerformed(ActionEvent e)
3020 viewport.showAllHiddenColumns();
3021 alignPanel.paintAlignment(true, true);
3022 viewport.sendSelection();
3026 public void hideSelSequences_actionPerformed(ActionEvent e)
3028 viewport.hideAllSelectedSeqs();
3032 * called by key handler and the hide all/show all menu items
3037 protected void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
3040 boolean hide = false;
3041 SequenceGroup sg = viewport.getSelectionGroup();
3042 if (!toggleSeqs && !toggleCols)
3044 // Hide everything by the current selection - this is a hack - we do the
3045 // invert and then hide
3046 // first check that there will be visible columns after the invert.
3047 if (viewport.hasSelectedColumns() || (sg != null && sg.getSize() > 0
3048 && sg.getStartRes() <= sg.getEndRes()))
3050 // now invert the sequence set, if required - empty selection implies
3051 // that no hiding is required.
3054 invertSequenceMenuItem_actionPerformed(null);
3055 sg = viewport.getSelectionGroup();
3059 viewport.expandColSelection(sg, true);
3060 // finally invert the column selection and get the new sequence
3062 invertColSel_actionPerformed(null);
3069 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
3071 hideSelSequences_actionPerformed(null);
3074 else if (!(toggleCols && viewport.hasSelectedColumns()))
3076 showAllSeqs_actionPerformed(null);
3082 if (viewport.hasSelectedColumns())
3084 hideSelColumns_actionPerformed(null);
3087 viewport.setSelectionGroup(sg);
3092 showAllColumns_actionPerformed(null);
3101 * jalview.jbgui.GAlignFrame#hideAllButSelection_actionPerformed(java.awt.
3102 * event.ActionEvent)
3105 public void hideAllButSelection_actionPerformed(ActionEvent e)
3107 toggleHiddenRegions(false, false);
3108 viewport.sendSelection();
3115 * jalview.jbgui.GAlignFrame#hideAllSelection_actionPerformed(java.awt.event
3119 public void hideAllSelection_actionPerformed(ActionEvent e)
3121 SequenceGroup sg = viewport.getSelectionGroup();
3122 viewport.expandColSelection(sg, false);
3123 viewport.hideAllSelectedSeqs();
3124 viewport.hideSelectedColumns();
3125 alignPanel.updateLayout();
3126 alignPanel.paintAlignment(true, true);
3127 viewport.sendSelection();
3134 * jalview.jbgui.GAlignFrame#showAllhidden_actionPerformed(java.awt.event.
3138 public void showAllhidden_actionPerformed(ActionEvent e)
3140 viewport.showAllHiddenColumns();
3141 viewport.showAllHiddenSeqs();
3142 alignPanel.paintAlignment(true, true);
3143 viewport.sendSelection();
3147 public void hideSelColumns_actionPerformed(ActionEvent e)
3149 viewport.hideSelectedColumns();
3150 alignPanel.updateLayout();
3151 alignPanel.paintAlignment(true, true);
3152 viewport.sendSelection();
3156 public void hiddenMarkers_actionPerformed(ActionEvent e)
3158 viewport.setShowHiddenMarkers(hiddenMarkers.isSelected());
3169 protected void scaleAbove_actionPerformed(ActionEvent e)
3171 viewport.setScaleAboveWrapped(scaleAbove.isSelected());
3172 alignPanel.updateLayout();
3173 alignPanel.paintAlignment(true, false);
3183 protected void scaleLeft_actionPerformed(ActionEvent e)
3185 viewport.setScaleLeftWrapped(scaleLeft.isSelected());
3186 alignPanel.updateLayout();
3187 alignPanel.paintAlignment(true, false);
3197 protected void scaleRight_actionPerformed(ActionEvent e)
3199 viewport.setScaleRightWrapped(scaleRight.isSelected());
3200 alignPanel.updateLayout();
3201 alignPanel.paintAlignment(true, false);
3211 public void viewBoxesMenuItem_actionPerformed(ActionEvent e)
3213 viewport.setShowBoxes(viewBoxesMenuItem.isSelected());
3214 alignPanel.paintAlignment(false, false);
3224 public void viewTextMenuItem_actionPerformed(ActionEvent e)
3226 viewport.setShowText(viewTextMenuItem.isSelected());
3227 alignPanel.paintAlignment(false, false);
3237 protected void renderGapsMenuItem_actionPerformed(ActionEvent e)
3239 viewport.setRenderGaps(renderGapsMenuItem.isSelected());
3240 alignPanel.paintAlignment(false, false);
3243 public FeatureSettings featureSettings;
3246 public FeatureSettingsControllerI getFeatureSettingsUI()
3248 return featureSettings;
3252 public void featureSettings_actionPerformed(ActionEvent e)
3254 if (featureSettings != null)
3256 featureSettings.close();
3257 featureSettings = null;
3259 if (!showSeqFeatures.isSelected())
3261 // make sure features are actually displayed
3262 showSeqFeatures.setSelected(true);
3263 showSeqFeatures_actionPerformed(null);
3265 featureSettings = new FeatureSettings(this);
3269 * Set or clear 'Show Sequence Features'
3275 public void showSeqFeatures_actionPerformed(ActionEvent evt)
3277 viewport.setShowSequenceFeatures(showSeqFeatures.isSelected());
3278 alignPanel.paintAlignment(true, true);
3282 * Action on toggle of the 'Show annotations' menu item. This shows or hides
3283 * the annotations panel as a whole.
3285 * The options to show/hide all annotations should be enabled when the panel
3286 * is shown, and disabled when the panel is hidden.
3291 public void annotationPanelMenuItem_actionPerformed(ActionEvent e)
3293 final boolean setVisible = annotationPanelMenuItem.isSelected();
3294 viewport.setShowAnnotation(setVisible);
3295 this.showAllSeqAnnotations.setEnabled(setVisible);
3296 this.hideAllSeqAnnotations.setEnabled(setVisible);
3297 this.showAllAlAnnotations.setEnabled(setVisible);
3298 this.hideAllAlAnnotations.setEnabled(setVisible);
3299 alignPanel.updateLayout();
3303 public void alignmentProperties()
3306 StringBuffer contents = new AlignmentProperties(viewport.getAlignment())
3309 String content = MessageManager.formatMessage("label.html_content",
3311 { contents.toString() });
3314 if (Platform.isJS())
3316 JLabel textLabel = new JLabel();
3317 textLabel.setText(content);
3318 textLabel.setBackground(Color.WHITE);
3320 pane = new JPanel(new BorderLayout());
3321 ((JPanel) pane).setOpaque(true);
3322 pane.setBackground(Color.WHITE);
3323 ((JPanel) pane).add(textLabel, BorderLayout.NORTH);
3332 JEditorPane editPane = new JEditorPane("text/html", "");
3333 editPane.setEditable(false);
3334 editPane.setText(content);
3338 JInternalFrame frame = new JInternalFrame();
3340 frame.getContentPane().add(new JScrollPane(pane));
3342 Desktop.addInternalFrame(frame, MessageManager
3343 .formatMessage("label.alignment_properties", new Object[]
3344 { getTitle() }), 500, 400);
3354 public void overviewMenuItem_actionPerformed(ActionEvent e)
3356 if (alignPanel.overviewPanel != null)
3361 JInternalFrame frame = new JInternalFrame();
3362 final OverviewPanel overview = new OverviewPanel(alignPanel);
3363 frame.setContentPane(overview);
3364 Desktop.addInternalFrame(frame, MessageManager
3365 .formatMessage("label.overview_params", new Object[]
3366 { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
3369 frame.setLayer(JLayeredPane.PALETTE_LAYER);
3370 frame.addInternalFrameListener(
3371 new javax.swing.event.InternalFrameAdapter()
3374 public void internalFrameClosed(
3375 javax.swing.event.InternalFrameEvent evt)
3378 alignPanel.setOverviewPanel(null);
3381 if (getKeyListeners().length > 0)
3383 frame.addKeyListener(getKeyListeners()[0]);
3386 alignPanel.setOverviewPanel(overview);
3390 public void textColour_actionPerformed()
3392 new TextColourChooser().chooseColour(alignPanel, null);
3396 * public void covariationColour_actionPerformed() {
3398 * CovariationColourScheme(viewport.getAlignment().getAlignmentAnnotation
3402 public void annotationColour_actionPerformed()
3404 new AnnotationColourChooser(viewport, alignPanel);
3408 public void annotationColumn_actionPerformed(ActionEvent e)
3410 new AnnotationColumnChooser(viewport, alignPanel);
3414 * Action on the user checking or unchecking the option to apply the selected
3415 * colour scheme to all groups. If unchecked, groups may have their own
3416 * independent colour schemes.
3421 public void applyToAllGroups_actionPerformed(boolean selected)
3423 viewport.setColourAppliesToAllGroups(selected);
3427 * Action on user selecting a colour from the colour menu
3430 * the name (not the menu item label!) of the colour scheme
3433 public void changeColour_actionPerformed(String name)
3436 * 'User Defined' opens a panel to configure or load a
3437 * user-defined colour scheme
3439 if (ResidueColourScheme.USER_DEFINED_MENU.equals(name))
3441 new UserDefinedColours(alignPanel);
3446 * otherwise set the chosen colour scheme (or null for 'None')
3448 ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
3450 viewport.getAlignment(), viewport.getHiddenRepSequences());
3455 * Actions on setting or changing the alignment colour scheme
3460 public void changeColour(ColourSchemeI cs)
3462 // TODO: pull up to controller method
3463 ColourMenuHelper.setColourSelected(colourMenu, cs);
3465 viewport.setGlobalColourScheme(cs);
3467 alignPanel.paintAlignment(true, true);
3471 * Show the PID threshold slider panel
3474 protected void modifyPID_actionPerformed()
3476 SliderPanel.setPIDSliderSource(alignPanel, viewport.getResidueShading(),
3477 alignPanel.getViewName());
3478 SliderPanel.showPIDSlider();
3482 * Show the Conservation slider panel
3485 protected void modifyConservation_actionPerformed()
3487 SliderPanel.setConservationSlider(alignPanel,
3488 viewport.getResidueShading(), alignPanel.getViewName());
3489 SliderPanel.showConservationSlider();
3493 * Action on selecting or deselecting (Colour) By Conservation
3496 public void conservationMenuItem_actionPerformed(boolean selected)
3498 modifyConservation.setEnabled(selected);
3499 viewport.setConservationSelected(selected);
3500 viewport.getResidueShading().setConservationApplied(selected);
3502 changeColour(viewport.getGlobalColourScheme());
3505 modifyConservation_actionPerformed();
3509 SliderPanel.hideConservationSlider();
3514 * Action on selecting or deselecting (Colour) Above PID Threshold
3517 public void abovePIDThreshold_actionPerformed(boolean selected)
3519 modifyPID.setEnabled(selected);
3520 viewport.setAbovePIDThreshold(selected);
3523 viewport.getResidueShading().setThreshold(0,
3524 viewport.isIgnoreGapsConsensus());
3527 changeColour(viewport.getGlobalColourScheme());
3530 modifyPID_actionPerformed();
3534 SliderPanel.hidePIDSlider();
3545 public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)
3547 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3548 AlignmentSorter.sortByPID(viewport.getAlignment(),
3549 viewport.getAlignment().getSequenceAt(0));
3550 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
3551 viewport.getAlignment()));
3552 alignPanel.paintAlignment(true, false);
3562 public void sortIDMenuItem_actionPerformed(ActionEvent e)
3564 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3565 AlignmentSorter.sortByID(viewport.getAlignment());
3567 new OrderCommand("ID Sort", oldOrder, viewport.getAlignment()));
3568 alignPanel.paintAlignment(true, false);
3578 public void sortLengthMenuItem_actionPerformed(ActionEvent e)
3580 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3581 AlignmentSorter.sortByLength(viewport.getAlignment());
3582 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
3583 viewport.getAlignment()));
3584 alignPanel.paintAlignment(true, false);
3594 public void sortGroupMenuItem_actionPerformed(ActionEvent e)
3596 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3597 AlignmentSorter.sortByGroup(viewport.getAlignment());
3598 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
3599 viewport.getAlignment()));
3601 alignPanel.paintAlignment(true, false);
3611 public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)
3613 new RedundancyPanel(alignPanel, this);
3623 public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)
3625 if ((viewport.getSelectionGroup() == null)
3626 || (viewport.getSelectionGroup().getSize() < 2))
3628 JvOptionPane.showInternalMessageDialog(this,
3629 MessageManager.getString(
3630 "label.you_must_select_least_two_sequences"),
3631 MessageManager.getString("label.invalid_selection"),
3632 JvOptionPane.WARNING_MESSAGE);
3636 JInternalFrame frame = new JInternalFrame();
3637 frame.setContentPane(new PairwiseAlignPanel(viewport));
3638 Desktop.addInternalFrame(frame,
3639 MessageManager.getString("action.pairwise_alignment"), 600,
3645 public void autoCalculate_actionPerformed(ActionEvent e)
3647 viewport.autoCalculateConsensus = autoCalculate.isSelected();
3648 if (viewport.autoCalculateConsensus)
3650 viewport.firePropertyChange("alignment", null,
3651 viewport.getAlignment().getSequences());
3656 public void sortByTreeOption_actionPerformed(ActionEvent e)
3658 viewport.sortByTree = sortByTree.isSelected();
3662 protected void listenToViewSelections_actionPerformed(ActionEvent e)
3664 viewport.followSelection = listenToViewSelections.isSelected();
3668 * Constructs a tree panel and adds it to the desktop
3671 * tree type (NJ or AV)
3673 * name of score model used to compute the tree
3675 * parameters for the distance or similarity calculation
3677 void newTreePanel(String type, String modelName,
3678 SimilarityParamsI options)
3680 String frameTitle = "";
3683 boolean onSelection = false;
3684 if (viewport.getSelectionGroup() != null
3685 && viewport.getSelectionGroup().getSize() > 0)
3687 SequenceGroup sg = viewport.getSelectionGroup();
3689 /* Decide if the selection is a column region */
3690 for (SequenceI _s : sg.getSequences())
3692 if (_s.getLength() < sg.getEndRes())
3694 JvOptionPane.showMessageDialog(Desktop.desktop,
3695 MessageManager.getString(
3696 "label.selected_region_to_tree_may_only_contain_residues_or_gaps"),
3697 MessageManager.getString(
3698 "label.sequences_selection_not_aligned"),
3699 JvOptionPane.WARNING_MESSAGE);
3708 if (viewport.getAlignment().getHeight() < 2)
3714 tp = new TreePanel(alignPanel, type, modelName, options);
3715 frameTitle = tp.getPanelTitle() + (onSelection ? " on region" : "");
3717 frameTitle += " from ";
3719 if (viewport.getViewName() != null)
3721 frameTitle += viewport.getViewName() + " of ";
3724 frameTitle += this.title;
3726 Desktop.addInternalFrame(tp, frameTitle, 600, 500);
3737 public void addSortByOrderMenuItem(String title,
3738 final AlignmentOrder order)
3740 final JMenuItem item = new JMenuItem(MessageManager
3741 .formatMessage("action.by_title_param", new Object[]
3744 item.addActionListener(new java.awt.event.ActionListener()
3747 public void actionPerformed(ActionEvent e)
3749 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3751 // TODO: JBPNote - have to map order entries to curent SequenceI
3753 AlignmentSorter.sortBy(viewport.getAlignment(), order);
3755 addHistoryItem(new OrderCommand(order.getName(), oldOrder,
3756 viewport.getAlignment()));
3758 alignPanel.paintAlignment(true, false);
3764 * Add a new sort by annotation score menu item
3767 * the menu to add the option to
3769 * the label used to retrieve scores for each sequence on the
3772 public void addSortByAnnotScoreMenuItem(JMenu sort,
3773 final String scoreLabel)
3775 final JMenuItem item = new JMenuItem(scoreLabel);
3777 item.addActionListener(new java.awt.event.ActionListener()
3780 public void actionPerformed(ActionEvent e)
3782 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3783 AlignmentSorter.sortByAnnotationScore(scoreLabel,
3784 viewport.getAlignment());// ,viewport.getSelectionGroup());
3785 addHistoryItem(new OrderCommand("Sort by " + scoreLabel, oldOrder,
3786 viewport.getAlignment()));
3787 alignPanel.paintAlignment(true, false);
3793 * last hash for alignment's annotation array - used to minimise cost of
3796 protected int _annotationScoreVectorHash;
3799 * search the alignment and rebuild the sort by annotation score submenu the
3800 * last alignment annotation vector hash is stored to minimize cost of
3801 * rebuilding in subsequence calls.
3805 public void buildSortByAnnotationScoresMenu()
3807 if (viewport.getAlignment().getAlignmentAnnotation() == null)
3812 if (viewport.getAlignment().getAlignmentAnnotation()
3813 .hashCode() != _annotationScoreVectorHash)
3815 sortByAnnotScore.removeAll();
3816 // almost certainly a quicker way to do this - but we keep it simple
3817 Hashtable<String, String> scoreSorts = new Hashtable<>();
3818 AlignmentAnnotation aann[];
3819 for (SequenceI sqa : viewport.getAlignment().getSequences())
3821 aann = sqa.getAnnotation();
3822 for (int i = 0; aann != null && i < aann.length; i++)
3824 if (aann[i].hasScore() && aann[i].sequenceRef != null)
3826 scoreSorts.put(aann[i].label, aann[i].label);
3830 Enumeration<String> labels = scoreSorts.keys();
3831 while (labels.hasMoreElements())
3833 addSortByAnnotScoreMenuItem(sortByAnnotScore,
3834 labels.nextElement());
3836 sortByAnnotScore.setVisible(scoreSorts.size() > 0);
3839 _annotationScoreVectorHash = viewport.getAlignment()
3840 .getAlignmentAnnotation().hashCode();
3845 * Maintain the Order by->Displayed Tree menu. Creates a new menu item for a
3846 * TreePanel with an appropriate <code>jalview.analysis.AlignmentSorter</code>
3847 * call. Listeners are added to remove the menu item when the treePanel is
3848 * closed, and adjust the tree leaf to sequence mapping when the alignment is
3852 public void buildTreeSortMenu()
3854 sortByTreeMenu.removeAll();
3856 List<Component> comps = PaintRefresher.components
3857 .get(viewport.getSequenceSetId());
3858 List<TreePanel> treePanels = new ArrayList<>();
3859 for (Component comp : comps)
3861 if (comp instanceof TreePanel)
3863 treePanels.add((TreePanel) comp);
3867 if (treePanels.size() < 1)
3869 sortByTreeMenu.setVisible(false);
3873 sortByTreeMenu.setVisible(true);
3875 for (final TreePanel tp : treePanels)
3877 final JMenuItem item = new JMenuItem(tp.getTitle());
3878 item.addActionListener(new java.awt.event.ActionListener()
3881 public void actionPerformed(ActionEvent e)
3883 tp.sortByTree_actionPerformed();
3884 addHistoryItem(tp.sortAlignmentIn(alignPanel));
3889 sortByTreeMenu.add(item);
3893 public boolean sortBy(AlignmentOrder alorder, String undoname)
3895 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
3896 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
3897 if (undoname != null)
3899 addHistoryItem(new OrderCommand(undoname, oldOrder,
3900 viewport.getAlignment()));
3902 alignPanel.paintAlignment(true, false);
3907 * Work out whether the whole set of sequences or just the selected set will
3908 * be submitted for multiple alignment.
3911 public jalview.datamodel.AlignmentView gatherSequencesForAlignment()
3913 // Now, check we have enough sequences
3914 AlignmentView msa = null;
3916 if ((viewport.getSelectionGroup() != null)
3917 && (viewport.getSelectionGroup().getSize() > 1))
3919 // JBPNote UGLY! To prettify, make SequenceGroup and Alignment conform to
3920 // some common interface!
3922 * SequenceGroup seqs = viewport.getSelectionGroup(); int sz; msa = new
3923 * SequenceI[sz = seqs.getSize(false)];
3925 * for (int i = 0; i < sz; i++) { msa[i] = (SequenceI)
3926 * seqs.getSequenceAt(i); }
3928 msa = viewport.getAlignmentView(true);
3930 else if (viewport.getSelectionGroup() != null
3931 && viewport.getSelectionGroup().getSize() == 1)
3933 int option = JvOptionPane.showConfirmDialog(this,
3934 MessageManager.getString("warn.oneseq_msainput_selection"),
3935 MessageManager.getString("label.invalid_selection"),
3936 JvOptionPane.OK_CANCEL_OPTION);
3937 if (option == JvOptionPane.OK_OPTION)
3939 msa = viewport.getAlignmentView(false);
3944 msa = viewport.getAlignmentView(false);
3950 * Decides what is submitted to a secondary structure prediction service: the
3951 * first sequence in the alignment, or in the current selection, or, if the
3952 * alignment is 'aligned' (ie padded with gaps), then the currently selected
3953 * region or the whole alignment. (where the first sequence in the set is the
3954 * one that the prediction will be for).
3956 public AlignmentView gatherSeqOrMsaForSecStrPrediction()
3958 AlignmentView seqs = null;
3960 if ((viewport.getSelectionGroup() != null)
3961 && (viewport.getSelectionGroup().getSize() > 0))
3963 seqs = viewport.getAlignmentView(true);
3967 seqs = viewport.getAlignmentView(false);
3969 // limit sequences - JBPNote in future - could spawn multiple prediction
3971 // TODO: viewport.getAlignment().isAligned is a global state - the local
3972 // selection may well be aligned - we preserve 2.0.8 behaviour for moment.
3973 if (!viewport.getAlignment().isAligned(false))
3975 seqs.setSequences(new SeqCigar[] { seqs.getSequences()[0] });
3976 // TODO: if seqs.getSequences().length>1 then should really have warned
3990 protected void loadTreeMenuItem_actionPerformed(ActionEvent e)
3992 // Pick the tree file
3993 JalviewFileChooser chooser = new JalviewFileChooser(
3994 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
3995 chooser.setFileView(new JalviewFileView());
3996 chooser.setDialogTitle(
3997 MessageManager.getString("label.select_newick_like_tree_file"));
3998 chooser.setToolTipText(
3999 MessageManager.getString("label.load_tree_file"));
4001 chooser.setResponseHandler(0,new Runnable()
4006 String filePath = chooser.getSelectedFile().getPath();
4007 Cache.setProperty("LAST_DIRECTORY", filePath);
4008 NewickFile fin = null;
4011 fin = new NewickFile(new FileParse(chooser.getSelectedFile(),
4012 DataSourceType.FILE));
4013 viewport.setCurrentTree(showNewickTree(fin, filePath).getTree());
4014 } catch (Exception ex)
4016 JvOptionPane.showMessageDialog(Desktop.desktop, ex.getMessage(),
4018 .getString("label.problem_reading_tree_file"),
4019 JvOptionPane.WARNING_MESSAGE);
4020 ex.printStackTrace();
4022 if (fin != null && fin.hasWarningMessage())
4024 JvOptionPane.showMessageDialog(Desktop.desktop,
4025 fin.getWarningMessage(),
4026 MessageManager.getString(
4027 "label.possible_problem_with_tree_file"),
4028 JvOptionPane.WARNING_MESSAGE);
4032 chooser.showOpenDialog(this);
4035 public TreePanel showNewickTree(NewickFile nf, String treeTitle)
4037 return showNewickTree(nf, treeTitle, 600, 500, 4, 5);
4040 public TreePanel showNewickTree(NewickFile nf, String treeTitle, int w,
4041 int h, int x, int y)
4043 return showNewickTree(nf, treeTitle, null, w, h, x, y);
4047 * Add a treeviewer for the tree extracted from a Newick file object to the
4048 * current alignment view
4055 * Associated alignment input data (or null)
4064 * @return TreePanel handle
4066 public TreePanel showNewickTree(NewickFile nf, String treeTitle,
4067 AlignmentView input, int w, int h, int x, int y)
4069 TreePanel tp = null;
4075 if (nf.getTree() != null)
4077 tp = new TreePanel(alignPanel, nf, treeTitle, input);
4083 tp.setLocation(x, y);
4086 Desktop.addInternalFrame(tp, treeTitle, w, h);
4088 } catch (Exception ex)
4090 ex.printStackTrace();
4096 private boolean buildingMenu = false;
4099 * Generates menu items and listener event actions for web service clients
4102 public void BuildWebServiceMenu()
4104 while (buildingMenu)
4108 System.err.println("Waiting for building menu to finish.");
4110 } catch (Exception e)
4114 final AlignFrame me = this;
4115 buildingMenu = true;
4116 new Thread(new Runnable()
4121 final List<JMenuItem> legacyItems = new ArrayList<>();
4124 // System.err.println("Building ws menu again "
4125 // + Thread.currentThread());
4126 // TODO: add support for context dependent disabling of services based
4128 // alignment and current selection
4129 // TODO: add additional serviceHandle parameter to specify abstract
4131 // class independently of AbstractName
4132 // TODO: add in rediscovery GUI function to restart discoverer
4133 // TODO: group services by location as well as function and/or
4135 // object broker mechanism.
4136 final Vector<JMenu> wsmenu = new Vector<>();
4137 final IProgressIndicator af = me;
4140 * do not i18n these strings - they are hard-coded in class
4141 * compbio.data.msa.Category, Jws2Discoverer.isRecalculable() and
4142 * SequenceAnnotationWSClient.initSequenceAnnotationWSClient()
4144 final JMenu msawsmenu = new JMenu("Alignment");
4145 final JMenu secstrmenu = new JMenu(
4146 "Secondary Structure Prediction");
4147 final JMenu seqsrchmenu = new JMenu("Sequence Database Search");
4148 final JMenu analymenu = new JMenu("Analysis");
4149 final JMenu dismenu = new JMenu("Protein Disorder");
4150 // JAL-940 - only show secondary structure prediction services from
4151 // the legacy server
4152 if (// Cache.getDefault("SHOW_JWS1_SERVICES", true)
4154 Discoverer.services != null && (Discoverer.services.size() > 0))
4156 // TODO: refactor to allow list of AbstractName/Handler bindings to
4158 // stored or retrieved from elsewhere
4159 // No MSAWS used any more:
4160 // Vector msaws = null; // (Vector)
4161 // Discoverer.services.get("MsaWS");
4162 Vector<ServiceHandle> secstrpr = Discoverer.services
4164 if (secstrpr != null)
4166 // Add any secondary structure prediction services
4167 for (int i = 0, j = secstrpr.size(); i < j; i++)
4169 final ext.vamsas.ServiceHandle sh = secstrpr
4171 jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
4172 .getServiceClient(sh);
4173 int p = secstrmenu.getItemCount();
4174 impl.attachWSMenuEntry(secstrmenu, me);
4175 int q = secstrmenu.getItemCount();
4176 for (int litm = p; litm < q; litm++)
4178 legacyItems.add(secstrmenu.getItem(litm));
4184 // Add all submenus in the order they should appear on the web
4186 wsmenu.add(msawsmenu);
4187 wsmenu.add(secstrmenu);
4188 wsmenu.add(dismenu);
4189 wsmenu.add(analymenu);
4190 // No search services yet
4191 // wsmenu.add(seqsrchmenu);
4193 javax.swing.SwingUtilities.invokeLater(new Runnable()
4200 webService.removeAll();
4201 // first, add discovered services onto the webservices menu
4202 if (wsmenu.size() > 0)
4204 for (int i = 0, j = wsmenu.size(); i < j; i++)
4206 webService.add(wsmenu.get(i));
4211 webService.add(me.webServiceNoServices);
4213 // TODO: move into separate menu builder class.
4214 boolean new_sspred = false;
4215 if (Cache.getDefault("SHOW_JWS2_SERVICES", true))
4217 Jws2Discoverer jws2servs = Jws2Discoverer.getDiscoverer();
4218 if (jws2servs != null)
4220 if (jws2servs.hasServices())
4222 jws2servs.attachWSMenuEntry(webService, me);
4223 for (Jws2Instance sv : jws2servs.getServices())
4225 if (sv.description.toLowerCase().contains("jpred"))
4227 for (JMenuItem jmi : legacyItems)
4229 jmi.setVisible(false);
4235 if (jws2servs.isRunning())
4237 JMenuItem tm = new JMenuItem(
4238 "Still discovering JABA Services");
4239 tm.setEnabled(false);
4244 build_urlServiceMenu(me.webService);
4245 build_fetchdbmenu(webService);
4246 for (JMenu item : wsmenu)
4248 if (item.getItemCount() == 0)
4250 item.setEnabled(false);
4254 item.setEnabled(true);
4257 } catch (Exception e)
4260 "Exception during web service menu building process.",
4265 } catch (Exception e)
4268 buildingMenu = false;
4275 * construct any groupURL type service menu entries.
4279 protected void build_urlServiceMenu(JMenu webService)
4281 // TODO: remove this code when 2.7 is released
4282 // DEBUG - alignmentView
4284 * JMenuItem testAlView = new JMenuItem("Test AlignmentView"); final
4285 * AlignFrame af = this; testAlView.addActionListener(new ActionListener() {
4287 * @Override public void actionPerformed(ActionEvent e) {
4288 * jalview.datamodel.AlignmentView
4289 * .testSelectionViews(af.viewport.getAlignment(),
4290 * af.viewport.getColumnSelection(), af.viewport.selectionGroup); }
4292 * }); webService.add(testAlView);
4294 // TODO: refactor to RestClient discoverer and merge menu entries for
4295 // rest-style services with other types of analysis/calculation service
4296 // SHmmr test client - still being implemented.
4297 // DEBUG - alignmentView
4299 for (jalview.ws.rest.RestClient client : jalview.ws.rest.RestClient
4302 client.attachWSMenuEntry(
4303 JvSwingUtils.findOrCreateMenu(webService, client.getAction()),
4309 * Searches the alignment sequences for xRefs and builds the Show
4310 * Cross-References menu (formerly called Show Products), with database
4311 * sources for which cross-references are found (protein sources for a
4312 * nucleotide alignment and vice versa)
4314 * @return true if Show Cross-references menu should be enabled
4316 public boolean canShowProducts()
4318 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
4319 AlignmentI dataset = viewport.getAlignment().getDataset();
4321 showProducts.removeAll();
4322 final boolean dna = viewport.getAlignment().isNucleotide();
4324 if (seqs == null || seqs.length == 0)
4326 // nothing to see here.
4330 boolean showp = false;
4333 List<String> ptypes = new CrossRef(seqs, dataset)
4334 .findXrefSourcesForSequences(dna);
4336 for (final String source : ptypes)
4339 final AlignFrame af = this;
4340 JMenuItem xtype = new JMenuItem(source);
4341 xtype.addActionListener(new ActionListener()
4344 public void actionPerformed(ActionEvent e)
4346 showProductsFor(af.viewport.getSequenceSelection(), dna,
4350 showProducts.add(xtype);
4352 showProducts.setVisible(showp);
4353 showProducts.setEnabled(showp);
4354 } catch (Exception e)
4357 "canShowProducts threw an exception - please report to help@jalview.org",
4365 * Finds and displays cross-references for the selected sequences (protein
4366 * products for nucleotide sequences, dna coding sequences for peptides).
4369 * the sequences to show cross-references for
4371 * true if from a nucleotide alignment (so showing proteins)
4373 * the database to show cross-references for
4375 protected void showProductsFor(final SequenceI[] sel, final boolean _odna,
4376 final String source)
4378 new Thread(CrossRefAction.getHandlerFor(sel, _odna, source, this))
4383 * Construct and display a new frame containing the translation of this
4384 * frame's DNA sequences to their aligned protein (amino acid) equivalents.
4387 public void showTranslation_actionPerformed(GeneticCodeI codeTable)
4389 AlignmentI al = null;
4392 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
4394 al = dna.translateCdna(codeTable);
4395 } catch (Exception ex)
4397 jalview.bin.Cache.log.error(
4398 "Exception during translation. Please report this !", ex);
4399 final String msg = MessageManager.getString(
4400 "label.error_when_translating_sequences_submit_bug_report");
4401 final String errorTitle = MessageManager
4402 .getString("label.implementation_error")
4403 + MessageManager.getString("label.translation_failed");
4404 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4405 JvOptionPane.ERROR_MESSAGE);
4408 if (al == null || al.getHeight() == 0)
4410 final String msg = MessageManager.getString(
4411 "label.select_at_least_three_bases_in_at_least_one_sequence_to_cDNA_translation");
4412 final String errorTitle = MessageManager
4413 .getString("label.translation_failed");
4414 JvOptionPane.showMessageDialog(Desktop.desktop, msg, errorTitle,
4415 JvOptionPane.WARNING_MESSAGE);
4419 AlignFrame af = new AlignFrame(al, DEFAULT_WIDTH, DEFAULT_HEIGHT);
4420 af.setFileFormat(this.currentFileFormat);
4421 final String newTitle = MessageManager
4422 .formatMessage("label.translation_of_params", new Object[]
4423 { this.getTitle(), codeTable.getId() });
4424 af.setTitle(newTitle);
4425 if (Cache.getDefault(Preferences.ENABLE_SPLIT_FRAME, true))
4427 final SequenceI[] seqs = viewport.getSelectionAsNewSequence();
4428 viewport.openSplitFrame(af, new Alignment(seqs));
4432 Desktop.addInternalFrame(af, newTitle, DEFAULT_WIDTH,
4439 * Set the file format
4443 public void setFileFormat(FileFormatI format)
4445 this.currentFileFormat = format;
4449 * Try to load a features file onto the alignment.
4452 * contents or path to retrieve file or a File object
4454 * access mode of file (see jalview.io.AlignFile)
4455 * @return true if features file was parsed correctly.
4457 public boolean parseFeaturesFile(Object file, DataSourceType sourceType)
4460 return avc.parseFeaturesFile(file, sourceType,
4461 Cache.getDefault("RELAXEDSEQIDMATCHING", false));
4466 public void refreshFeatureUI(boolean enableIfNecessary)
4468 // note - currently this is only still here rather than in the controller
4469 // because of the featureSettings hard reference that is yet to be
4471 if (enableIfNecessary)
4473 viewport.setShowSequenceFeatures(true);
4474 showSeqFeatures.setSelected(true);
4480 public void dragEnter(DropTargetDragEvent evt)
4485 public void dragExit(DropTargetEvent evt)
4490 public void dragOver(DropTargetDragEvent evt)
4495 public void dropActionChanged(DropTargetDragEvent evt)
4500 public void drop(DropTargetDropEvent evt)
4502 // JAL-1552 - acceptDrop required before getTransferable call for
4503 // Java's Transferable for native dnd
4504 evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);
4505 Transferable t = evt.getTransferable();
4507 final AlignFrame thisaf = this;
4508 final List<Object> files = new ArrayList<>();
4509 List<DataSourceType> protocols = new ArrayList<>();
4513 Desktop.transferFromDropTarget(files, protocols, evt, t);
4514 } catch (Exception e)
4516 e.printStackTrace();
4520 new Thread(new Runnable()
4527 // check to see if any of these files have names matching sequences
4530 SequenceIdMatcher idm = new SequenceIdMatcher(
4531 viewport.getAlignment().getSequencesArray());
4533 * Object[] { String,SequenceI}
4535 ArrayList<Object[]> filesmatched = new ArrayList<>();
4536 ArrayList<Object> filesnotmatched = new ArrayList<>();
4537 for (int i = 0; i < files.size(); i++)
4540 Object file = files.get(i);
4541 String fileName = file.toString();
4543 DataSourceType protocol = (file instanceof File
4544 ? DataSourceType.FILE
4545 : FormatAdapter.checkProtocol(fileName));
4546 if (protocol == DataSourceType.FILE)
4549 if (file instanceof File) {
4551 Platform.cacheFileData(fl);
4553 fl = new File(fileName);
4555 pdbfn = fl.getName();
4557 else if (protocol == DataSourceType.URL)
4559 URL url = new URL(fileName);
4560 pdbfn = url.getFile();
4562 if (pdbfn.length() > 0)
4564 // attempt to find a match in the alignment
4565 SequenceI[] mtch = idm.findAllIdMatches(pdbfn);
4566 int l = 0, c = pdbfn.indexOf(".");
4567 while (mtch == null && c != -1)
4572 } while ((c = pdbfn.indexOf(".", l)) > l);
4575 pdbfn = pdbfn.substring(0, l);
4577 mtch = idm.findAllIdMatches(pdbfn);
4584 type = new IdentifyFile().identify(file, protocol);
4585 } catch (Exception ex)
4589 if (type != null && type.isStructureFile())
4591 filesmatched.add(new Object[] { file, protocol, mtch });
4595 // File wasn't named like one of the sequences or wasn't a PDB
4597 filesnotmatched.add(file);
4601 if (filesmatched.size() > 0)
4603 boolean autoAssociate = Cache
4604 .getDefault("AUTOASSOCIATE_PDBANDSEQS", false);
4607 String msg = MessageManager.formatMessage(
4608 "label.automatically_associate_structure_files_with_sequences_same_name",
4610 { Integer.valueOf(filesmatched.size())
4612 String ttl = MessageManager.getString(
4613 "label.automatically_associate_structure_files_by_name");
4614 int choice = JvOptionPane.showConfirmDialog(thisaf, msg,
4615 ttl, JvOptionPane.YES_NO_OPTION);
4616 autoAssociate = choice == JvOptionPane.YES_OPTION;
4620 for (Object[] fm : filesmatched)
4622 // try and associate
4623 // TODO: may want to set a standard ID naming formalism for
4624 // associating PDB files which have no IDs.
4625 for (SequenceI toassoc : (SequenceI[]) fm[2])
4627 PDBEntry pe = new AssociatePdbFileWithSeq()
4628 .associatePdbWithSeq(fm[0].toString(),
4629 (DataSourceType) fm[1], toassoc, false,
4633 System.err.println("Associated file : "
4634 + (fm[0].toString()) + " with "
4635 + toassoc.getDisplayId(true));
4639 // TODO: do we need to update overview ? only if features are
4641 alignPanel.paintAlignment(true, false);
4647 * add declined structures as sequences
4649 for (Object[] o : filesmatched)
4651 filesnotmatched.add(o[0]);
4655 if (filesnotmatched.size() > 0)
4657 if (assocfiles > 0 && (Cache.getDefault(
4658 "AUTOASSOCIATE_PDBANDSEQS_IGNOREOTHERS", false)
4659 || JvOptionPane.showConfirmDialog(thisaf,
4660 "<html>" + MessageManager.formatMessage(
4661 "label.ignore_unmatched_dropped_files_info",
4664 filesnotmatched.size())
4667 MessageManager.getString(
4668 "label.ignore_unmatched_dropped_files"),
4669 JvOptionPane.YES_NO_OPTION) == JvOptionPane.YES_OPTION))
4673 for (Object fn : filesnotmatched)
4675 loadJalviewDataFile(fn, null, null, null);
4679 } catch (Exception ex)
4681 ex.printStackTrace();
4689 * Attempt to load a "dropped" file or URL string, by testing in turn for
4691 * <li>an Annotation file</li>
4692 * <li>a JNet file</li>
4693 * <li>a features file</li>
4694 * <li>else try to interpret as an alignment file</li>
4698 * either a filename or a URL string.
4700 public void loadJalviewDataFile(Object file, DataSourceType sourceType,
4701 FileFormatI format, SequenceI assocSeq)
4703 // BH 2018 was String file
4706 if (sourceType == null)
4708 sourceType = FormatAdapter.checkProtocol(file);
4710 // if the file isn't identified, or not positively identified as some
4711 // other filetype (PFAM is default unidentified alignment file type) then
4712 // try to parse as annotation.
4713 boolean isAnnotation = (format == null
4714 || FileFormat.Pfam.equals(format))
4715 ? new AnnotationFile().annotateAlignmentView(viewport,
4721 // first see if its a T-COFFEE score file
4722 TCoffeeScoreFile tcf = null;
4725 tcf = new TCoffeeScoreFile(file, sourceType);
4728 if (tcf.annotateAlignment(viewport.getAlignment(), true))
4732 new TCoffeeColourScheme(viewport.getAlignment()));
4733 isAnnotation = true;
4734 setStatus(MessageManager.getString(
4735 "label.successfully_pasted_tcoffee_scores_to_alignment"));
4739 // some problem - if no warning its probable that the ID matching
4740 // process didn't work
4741 JvOptionPane.showMessageDialog(Desktop.desktop,
4742 tcf.getWarningMessage() == null
4743 ? MessageManager.getString(
4744 "label.check_file_matches_sequence_ids_alignment")
4745 : tcf.getWarningMessage(),
4746 MessageManager.getString(
4747 "label.problem_reading_tcoffee_score_file"),
4748 JvOptionPane.WARNING_MESSAGE);
4755 } catch (Exception x)
4758 "Exception when processing data source as T-COFFEE score file",
4764 // try to see if its a JNet 'concise' style annotation file *before*
4766 // try to parse it as a features file
4769 format = new IdentifyFile().identify(file, sourceType);
4771 if (FileFormat.ScoreMatrix == format)
4773 ScoreMatrixFile sm = new ScoreMatrixFile(
4774 new FileParse(file, sourceType));
4776 // todo: i18n this message
4777 setStatus(MessageManager.formatMessage(
4778 "label.successfully_loaded_matrix",
4779 sm.getMatrixName()));
4781 else if (FileFormat.Jnet.equals(format))
4783 JPredFile predictions = new JPredFile(file, sourceType);
4784 new JnetAnnotationMaker();
4785 JnetAnnotationMaker.add_annotation(predictions,
4786 viewport.getAlignment(), 0, false);
4787 viewport.getAlignment().setupJPredAlignment();
4788 isAnnotation = true;
4790 // else if (IdentifyFile.FeaturesFile.equals(format))
4791 else if (FileFormat.Features.equals(format))
4793 if (parseFeaturesFile(file, sourceType))
4795 alignPanel.paintAlignment(true, true);
4800 new FileLoader().LoadFile(viewport, file, sourceType, format);
4807 alignPanel.adjustAnnotationHeight();
4808 viewport.updateSequenceIdColours();
4809 buildSortByAnnotationScoresMenu();
4810 alignPanel.paintAlignment(true, true);
4812 } catch (Exception ex)
4814 ex.printStackTrace();
4815 } catch (OutOfMemoryError oom)
4820 } catch (Exception x)
4825 + (sourceType != null
4826 ? (sourceType == DataSourceType.PASTE
4828 : "using " + sourceType + " from "
4832 ? "(parsing as '" + format + "' file)"
4834 oom, Desktop.desktop);
4839 * Method invoked by the ChangeListener on the tabbed pane, in other words
4840 * when a different tabbed pane is selected by the user or programmatically.
4843 public void tabSelectionChanged(int index)
4847 alignPanel = alignPanels.get(index);
4848 viewport = alignPanel.av;
4849 avc.setViewportAndAlignmentPanel(viewport, alignPanel);
4850 setMenusFromViewport(viewport);
4854 * 'focus' any colour slider that is open to the selected viewport
4856 if (viewport.getConservationSelected())
4858 SliderPanel.setConservationSlider(alignPanel,
4859 viewport.getResidueShading(), alignPanel.getViewName());
4863 SliderPanel.hideConservationSlider();
4865 if (viewport.getAbovePIDThreshold())
4867 SliderPanel.setPIDSliderSource(alignPanel,
4868 viewport.getResidueShading(), alignPanel.getViewName());
4872 SliderPanel.hidePIDSlider();
4876 * If there is a frame linked to this one in a SplitPane, switch it to the
4877 * same view tab index. No infinite recursion of calls should happen, since
4878 * tabSelectionChanged() should not get invoked on setting the selected
4879 * index to an unchanged value. Guard against setting an invalid index
4880 * before the new view peer tab has been created.
4882 final AlignViewportI peer = viewport.getCodingComplement();
4885 AlignFrame linkedAlignFrame = ((AlignViewport) peer)
4886 .getAlignPanel().alignFrame;
4887 if (linkedAlignFrame.tabbedPane.getTabCount() > index)
4889 linkedAlignFrame.tabbedPane.setSelectedIndex(index);
4895 * On right mouse click on view tab, prompt for and set new view name.
4898 public void tabbedPane_mousePressed(MouseEvent e)
4900 if (e.isPopupTrigger())
4902 String msg = MessageManager.getString("label.enter_view_name");
4903 String ttl = tabbedPane.getTitleAt(tabbedPane.getSelectedIndex());
4904 String reply = JvOptionPane.showInputDialog(msg, ttl);
4908 viewport.setViewName(reply);
4909 // TODO warn if reply is in getExistingViewNames()?
4910 tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
4915 public AlignViewport getCurrentView()
4921 * Open the dialog for regex description parsing.
4924 protected void extractScores_actionPerformed(ActionEvent e)
4926 ParseProperties pp = new jalview.analysis.ParseProperties(
4927 viewport.getAlignment());
4928 // TODO: verify regex and introduce GUI dialog for version 2.5
4929 // if (pp.getScoresFromDescription("col", "score column ",
4930 // "\\W*([-+]?\\d*\\.?\\d*e?-?\\d*)\\W+([-+]?\\d*\\.?\\d*e?-?\\d*)",
4932 if (pp.getScoresFromDescription("description column",
4933 "score in description column ", "\\W*([-+eE0-9.]+)", true) > 0)
4935 buildSortByAnnotationScoresMenu();
4943 * jalview.jbgui.GAlignFrame#showDbRefs_actionPerformed(java.awt.event.ActionEvent
4947 protected void showDbRefs_actionPerformed(ActionEvent e)
4949 viewport.setShowDBRefs(showDbRefsMenuitem.isSelected());
4955 * @seejalview.jbgui.GAlignFrame#showNpFeats_actionPerformed(java.awt.event.
4959 protected void showNpFeats_actionPerformed(ActionEvent e)
4961 viewport.setShowNPFeats(showNpFeatsMenuitem.isSelected());
4965 * find the viewport amongst the tabs in this alignment frame and close that
4970 public boolean closeView(AlignViewportI av)
4974 this.closeMenuItem_actionPerformed(false);
4977 Component[] comp = tabbedPane.getComponents();
4978 for (int i = 0; comp != null && i < comp.length; i++)
4980 if (comp[i] instanceof AlignmentPanel)
4982 if (((AlignmentPanel) comp[i]).av == av)
4985 closeView((AlignmentPanel) comp[i]);
4993 protected void build_fetchdbmenu(JMenu webService)
4995 // Temporary hack - DBRef Fetcher always top level ws entry.
4996 // TODO We probably want to store a sequence database checklist in
4997 // preferences and have checkboxes.. rather than individual sources selected
4999 final JMenu rfetch = new JMenu(
5000 MessageManager.getString("action.fetch_db_references"));
5001 rfetch.setToolTipText(MessageManager.getString(
5002 "label.retrieve_parse_sequence_database_records_alignment_or_selected_sequences"));
5003 webService.add(rfetch);
5005 final JCheckBoxMenuItem trimrs = new JCheckBoxMenuItem(
5006 MessageManager.getString("option.trim_retrieved_seqs"));
5007 trimrs.setToolTipText(
5008 MessageManager.getString("label.trim_retrieved_sequences"));
5010 Cache.getDefault(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES, true));
5011 trimrs.addActionListener(new ActionListener()
5014 public void actionPerformed(ActionEvent e)
5016 trimrs.setSelected(trimrs.isSelected());
5017 Cache.setProperty(DBRefFetcher.TRIM_RETRIEVED_SEQUENCES,
5018 Boolean.valueOf(trimrs.isSelected()).toString());
5022 JMenuItem fetchr = new JMenuItem(
5023 MessageManager.getString("label.standard_databases"));
5024 fetchr.setToolTipText(
5025 MessageManager.getString("label.fetch_embl_uniprot"));
5026 fetchr.addActionListener(new ActionListener()
5030 public void actionPerformed(ActionEvent e)
5032 new Thread(new Runnable()
5037 boolean isNucleotide = alignPanel.alignFrame.getViewport()
5038 .getAlignment().isNucleotide();
5039 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5040 alignPanel.av.getSequenceSelection(),
5041 alignPanel.alignFrame, null,
5042 alignPanel.alignFrame.featureSettings, isNucleotide);
5043 dbRefFetcher.addListener(new FetchFinishedListenerI()
5046 public void finished()
5049 for (FeatureSettingsModelI srcSettings : dbRefFetcher
5050 .getFeatureSettingsModels())
5053 alignPanel.av.mergeFeaturesStyle(srcSettings);
5055 AlignFrame.this.setMenusForViewport();
5058 dbRefFetcher.fetchDBRefs(false);
5066 new Thread(new Runnable()
5071 final jalview.ws.SequenceFetcher sf = jalview.gui.SequenceFetcher
5072 .getSequenceFetcherSingleton();
5073 javax.swing.SwingUtilities.invokeLater(new Runnable()
5078 String[] dbclasses = sf.getNonAlignmentSources();
5079 List<DbSourceProxy> otherdb;
5080 JMenu dfetch = new JMenu();
5081 JMenu ifetch = new JMenu();
5082 JMenuItem fetchr = null;
5083 int comp = 0, icomp = 0, mcomp = 15;
5084 String mname = null;
5086 for (String dbclass : dbclasses)
5088 otherdb = sf.getSourceProxy(dbclass);
5089 // add a single entry for this class, or submenu allowing 'fetch
5091 if (otherdb == null || otherdb.size() < 1)
5097 mname = "From " + dbclass;
5099 if (otherdb.size() == 1)
5101 final DbSourceProxy[] dassource = otherdb
5102 .toArray(new DbSourceProxy[0]);
5103 DbSourceProxy src = otherdb.get(0);
5104 fetchr = new JMenuItem(src.getDbSource());
5105 fetchr.addActionListener(new ActionListener()
5109 public void actionPerformed(ActionEvent e)
5111 new Thread(new Runnable()
5117 boolean isNucleotide = alignPanel.alignFrame
5118 .getViewport().getAlignment()
5120 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5121 alignPanel.av.getSequenceSelection(),
5122 alignPanel.alignFrame, dassource,
5123 alignPanel.alignFrame.featureSettings,
5126 .addListener(new FetchFinishedListenerI()
5129 public void finished()
5131 FeatureSettingsModelI srcSettings = dassource[0]
5132 .getFeatureColourScheme();
5133 alignPanel.av.mergeFeaturesStyle(
5135 AlignFrame.this.setMenusForViewport();
5138 dbRefFetcher.fetchDBRefs(false);
5144 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5145 MessageManager.formatMessage(
5146 "label.fetch_retrieve_from", new Object[]
5147 { src.getDbName() })));
5153 final DbSourceProxy[] dassource = otherdb
5154 .toArray(new DbSourceProxy[0]);
5156 DbSourceProxy src = otherdb.get(0);
5157 fetchr = new JMenuItem(MessageManager
5158 .formatMessage("label.fetch_all_param", new Object[]
5159 { src.getDbSource() }));
5160 fetchr.addActionListener(new ActionListener()
5163 public void actionPerformed(ActionEvent e)
5165 new Thread(new Runnable()
5171 boolean isNucleotide = alignPanel.alignFrame
5172 .getViewport().getAlignment()
5174 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5175 alignPanel.av.getSequenceSelection(),
5176 alignPanel.alignFrame, dassource,
5177 alignPanel.alignFrame.featureSettings,
5180 .addListener(new FetchFinishedListenerI()
5183 public void finished()
5185 AlignFrame.this.setMenusForViewport();
5188 dbRefFetcher.fetchDBRefs(false);
5194 fetchr.setToolTipText(JvSwingUtils.wrapTooltip(true,
5195 MessageManager.formatMessage(
5196 "label.fetch_retrieve_from_all_sources",
5198 { Integer.valueOf(otherdb.size())
5200 src.getDbSource(), src.getDbName() })));
5203 // and then build the rest of the individual menus
5204 ifetch = new JMenu(MessageManager.formatMessage(
5205 "label.source_from_db_source", new Object[]
5206 { src.getDbSource() }));
5208 String imname = null;
5210 for (DbSourceProxy sproxy : otherdb)
5212 String dbname = sproxy.getDbName();
5213 String sname = dbname.length() > 5
5214 ? dbname.substring(0, 5) + "..."
5216 String msname = dbname.length() > 10
5217 ? dbname.substring(0, 10) + "..."
5221 imname = MessageManager
5222 .formatMessage("label.from_msname", new Object[]
5225 fetchr = new JMenuItem(msname);
5226 final DbSourceProxy[] dassrc = { sproxy };
5227 fetchr.addActionListener(new ActionListener()
5231 public void actionPerformed(ActionEvent e)
5233 new Thread(new Runnable()
5239 boolean isNucleotide = alignPanel.alignFrame
5240 .getViewport().getAlignment()
5242 DBRefFetcher dbRefFetcher = new DBRefFetcher(
5243 alignPanel.av.getSequenceSelection(),
5244 alignPanel.alignFrame, dassrc,
5245 alignPanel.alignFrame.featureSettings,
5248 .addListener(new FetchFinishedListenerI()
5251 public void finished()
5253 AlignFrame.this.setMenusForViewport();
5256 dbRefFetcher.fetchDBRefs(false);
5262 fetchr.setToolTipText(
5263 "<html>" + MessageManager.formatMessage(
5264 "label.fetch_retrieve_from", new Object[]
5268 if (++icomp >= mcomp || i == (otherdb.size()))
5270 ifetch.setText(MessageManager.formatMessage(
5271 "label.source_to_target", imname, sname));
5273 ifetch = new JMenu();
5281 if (comp >= mcomp || dbi >= (dbclasses.length))
5283 dfetch.setText(MessageManager.formatMessage(
5284 "label.source_to_target", mname, dbclass));
5286 dfetch = new JMenu();
5299 * Left justify the whole alignment.
5302 protected void justifyLeftMenuItem_actionPerformed(ActionEvent e)
5304 AlignmentI al = viewport.getAlignment();
5306 viewport.firePropertyChange("alignment", null, al);
5310 * Right justify the whole alignment.
5313 protected void justifyRightMenuItem_actionPerformed(ActionEvent e)
5315 AlignmentI al = viewport.getAlignment();
5317 viewport.firePropertyChange("alignment", null, al);
5321 public void setShowSeqFeatures(boolean b)
5323 showSeqFeatures.setSelected(b);
5324 viewport.setShowSequenceFeatures(b);
5331 * jalview.jbgui.GAlignFrame#showUnconservedMenuItem_actionPerformed(java.
5332 * awt.event.ActionEvent)
5335 protected void showUnconservedMenuItem_actionPerformed(ActionEvent e)
5337 viewport.setShowUnconserved(showNonconservedMenuItem.getState());
5338 alignPanel.paintAlignment(false, false);
5345 * jalview.jbgui.GAlignFrame#showGroupConsensus_actionPerformed(java.awt.event
5349 protected void showGroupConsensus_actionPerformed(ActionEvent e)
5351 viewport.setShowGroupConsensus(showGroupConsensus.getState());
5352 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5360 * jalview.jbgui.GAlignFrame#showGroupConservation_actionPerformed(java.awt
5361 * .event.ActionEvent)
5364 protected void showGroupConservation_actionPerformed(ActionEvent e)
5366 viewport.setShowGroupConservation(showGroupConservation.getState());
5367 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5374 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
5375 * .event.ActionEvent)
5378 protected void showConsensusHistogram_actionPerformed(ActionEvent e)
5380 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
5381 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5388 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
5389 * .event.ActionEvent)
5392 protected void showSequenceLogo_actionPerformed(ActionEvent e)
5394 viewport.setShowSequenceLogo(showSequenceLogo.getState());
5395 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5399 protected void normaliseSequenceLogo_actionPerformed(ActionEvent e)
5401 showSequenceLogo.setState(true);
5402 viewport.setShowSequenceLogo(true);
5403 viewport.setNormaliseSequenceLogo(normaliseSequenceLogo.getState());
5404 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5408 protected void applyAutoAnnotationSettings_actionPerformed(ActionEvent e)
5410 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
5417 * jalview.jbgui.GAlignFrame#makeGrpsFromSelection_actionPerformed(java.awt
5418 * .event.ActionEvent)
5421 protected void makeGrpsFromSelection_actionPerformed(ActionEvent e)
5423 if (avc.makeGroupsFromSelection())
5425 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5426 alignPanel.updateAnnotation();
5427 alignPanel.paintAlignment(true,
5428 viewport.needToUpdateStructureViews());
5432 public void clearAlignmentSeqRep()
5434 // TODO refactor alignmentseqrep to controller
5435 if (viewport.getAlignment().hasSeqrep())
5437 viewport.getAlignment().setSeqrep(null);
5438 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
5439 alignPanel.updateAnnotation();
5440 alignPanel.paintAlignment(true, true);
5445 protected void createGroup_actionPerformed(ActionEvent e)
5447 if (avc.createGroup())
5449 if (applyAutoAnnotationSettings.isSelected())
5451 alignPanel.updateAnnotation(true, false);
5453 alignPanel.alignmentChanged();
5458 protected void unGroup_actionPerformed(ActionEvent e)
5462 alignPanel.alignmentChanged();
5467 * make the given alignmentPanel the currently selected tab
5469 * @param alignmentPanel
5471 public void setDisplayedView(AlignmentPanel alignmentPanel)
5473 if (!viewport.getSequenceSetId()
5474 .equals(alignmentPanel.av.getSequenceSetId()))
5476 throw new Error(MessageManager.getString(
5477 "error.implementation_error_cannot_show_view_alignment_frame"));
5479 if (tabbedPane != null && tabbedPane.getTabCount() > 0 && alignPanels
5480 .indexOf(alignmentPanel) != tabbedPane.getSelectedIndex())
5482 tabbedPane.setSelectedIndex(alignPanels.indexOf(alignmentPanel));
5487 * Action on selection of menu options to Show or Hide annotations.
5490 * @param forSequences
5491 * update sequence-related annotations
5492 * @param forAlignment
5493 * update non-sequence-related annotations
5496 protected void setAnnotationsVisibility(boolean visible,
5497 boolean forSequences, boolean forAlignment)
5499 AlignmentAnnotation[] anns = alignPanel.getAlignment()
5500 .getAlignmentAnnotation();
5505 for (AlignmentAnnotation aa : anns)
5508 * don't display non-positional annotations on an alignment
5510 if (aa.annotations == null)
5514 boolean apply = (aa.sequenceRef == null && forAlignment)
5515 || (aa.sequenceRef != null && forSequences);
5518 aa.visible = visible;
5521 alignPanel.validateAnnotationDimensions(true);
5522 alignPanel.alignmentChanged();
5526 * Store selected annotation sort order for the view and repaint.
5529 protected void sortAnnotations_actionPerformed()
5531 this.alignPanel.av.setSortAnnotationsBy(getAnnotationSortOrder());
5533 .setShowAutocalculatedAbove(isShowAutoCalculatedAbove());
5534 alignPanel.paintAlignment(false, false);
5539 * @return alignment panels in this alignment frame
5541 public List<? extends AlignmentViewPanel> getAlignPanels()
5543 // alignPanels is never null
5544 // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
5549 * Open a new alignment window, with the cDNA associated with this (protein)
5550 * alignment, aligned as is the protein.
5552 protected void viewAsCdna_actionPerformed()
5554 // TODO no longer a menu action - refactor as required
5555 final AlignmentI alignment = getViewport().getAlignment();
5556 List<AlignedCodonFrame> mappings = alignment.getCodonFrames();
5557 if (mappings == null)
5561 List<SequenceI> cdnaSeqs = new ArrayList<>();
5562 for (SequenceI aaSeq : alignment.getSequences())
5564 for (AlignedCodonFrame acf : mappings)
5566 SequenceI dnaSeq = acf.getDnaForAaSeq(aaSeq.getDatasetSequence());
5570 * There is a cDNA mapping for this protein sequence - add to new
5571 * alignment. It will share the same dataset sequence as other mapped
5572 * cDNA (no new mappings need to be created).
5574 final Sequence newSeq = new Sequence(dnaSeq);
5575 newSeq.setDatasetSequence(dnaSeq);
5576 cdnaSeqs.add(newSeq);
5580 if (cdnaSeqs.size() == 0)
5582 // show a warning dialog no mapped cDNA
5585 AlignmentI cdna = new Alignment(
5586 cdnaSeqs.toArray(new SequenceI[cdnaSeqs.size()]));
5587 GAlignFrame alignFrame = new AlignFrame(cdna, AlignFrame.DEFAULT_WIDTH,
5588 AlignFrame.DEFAULT_HEIGHT);
5589 cdna.alignAs(alignment);
5590 String newtitle = "cDNA " + MessageManager.getString("label.for") + " "
5592 Desktop.addInternalFrame(alignFrame, newtitle, AlignFrame.DEFAULT_WIDTH,
5593 AlignFrame.DEFAULT_HEIGHT);
5597 * Set visibility of dna/protein complement view (available when shown in a
5603 protected void showComplement_actionPerformed(boolean show)
5605 SplitContainerI sf = getSplitViewContainer();
5608 sf.setComplementVisible(this, show);
5613 * Generate the reverse (optionally complemented) of the selected sequences,
5614 * and add them to the alignment
5617 protected void showReverse_actionPerformed(boolean complement)
5619 AlignmentI al = null;
5622 Dna dna = new Dna(viewport, viewport.getViewAsVisibleContigs(true));
5623 al = dna.reverseCdna(complement);
5624 viewport.addAlignment(al, "");
5625 addHistoryItem(new EditCommand(
5626 MessageManager.getString("label.add_sequences"), Action.PASTE,
5627 al.getSequencesArray(), 0, al.getWidth(),
5628 viewport.getAlignment()));
5629 } catch (Exception ex)
5631 System.err.println(ex.getMessage());
5637 * Try to run a script in the Groovy console, having first ensured that this
5638 * AlignFrame is set as currentAlignFrame in Desktop, to allow the script to
5639 * be targeted at this alignment.
5642 protected void runGroovy_actionPerformed()
5644 Jalview.setCurrentAlignFrame(this);
5645 groovy.ui.Console console = Desktop.getGroovyConsole();
5646 if (console != null)
5650 console.runScript();
5651 } catch (Exception ex)
5653 System.err.println((ex.toString()));
5654 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
5655 MessageManager.getString("label.couldnt_run_groovy_script"),
5656 MessageManager.getString("label.groovy_support_failed"),
5657 JvOptionPane.ERROR_MESSAGE);
5662 System.err.println("Can't run Groovy script as console not found");
5667 * Hides columns containing (or not containing) a specified feature, provided
5668 * that would not leave all columns hidden
5670 * @param featureType
5671 * @param columnsContaining
5674 public boolean hideFeatureColumns(String featureType,
5675 boolean columnsContaining)
5677 boolean notForHiding = avc.markColumnsContainingFeatures(
5678 columnsContaining, false, false, featureType);
5681 if (avc.markColumnsContainingFeatures(!columnsContaining, false,
5682 false, featureType))
5684 getViewport().hideSelectedColumns();
5692 protected void selectHighlightedColumns_actionPerformed(
5693 ActionEvent actionEvent)
5695 // include key modifier check in case user selects from menu
5696 avc.markHighlightedColumns(
5697 (actionEvent.getModifiers() & ActionEvent.ALT_MASK) != 0, true,
5698 (actionEvent.getModifiers() & (ActionEvent.META_MASK
5699 | ActionEvent.CTRL_MASK)) != 0);
5703 * Rebuilds the Colour menu, including any user-defined colours which have
5704 * been loaded either on startup or during the session
5706 public void buildColourMenu()
5708 colourMenu.removeAll();
5710 colourMenu.add(applyToAllGroups);
5711 colourMenu.add(textColour);
5712 colourMenu.addSeparator();
5714 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this,
5715 viewport.getAlignment(), false);
5717 colourMenu.add(annotationColour);
5718 bg.add(annotationColour);
5719 colourMenu.addSeparator();
5720 colourMenu.add(conservationMenuItem);
5721 colourMenu.add(modifyConservation);
5722 colourMenu.add(abovePIDThreshold);
5723 colourMenu.add(modifyPID);
5725 ColourSchemeI colourScheme = viewport.getGlobalColourScheme();
5726 ColourMenuHelper.setColourSelected(colourMenu, colourScheme);
5730 * Open a dialog (if not already open) that allows the user to select and
5731 * calculate PCA or Tree analysis
5733 protected void openTreePcaDialog()
5735 if (alignPanel.getCalculationDialog() == null)
5737 new CalculationChooser(AlignFrame.this);
5742 protected void loadVcf_actionPerformed()
5744 JalviewFileChooser chooser = new JalviewFileChooser(
5745 Cache.getProperty("LAST_DIRECTORY"));
5746 chooser.setFileView(new JalviewFileView());
5747 chooser.setDialogTitle(MessageManager.getString("label.load_vcf_file"));
5748 chooser.setToolTipText(MessageManager.getString("label.load_vcf_file"));
5749 final AlignFrame us = this;
5750 chooser.setResponseHandler(0, new Runnable()
5755 String choice = chooser.getSelectedFile().getPath();
5756 Cache.setProperty("LAST_DIRECTORY", choice);
5757 SequenceI[] seqs = viewport.getAlignment().getSequencesArray();
5758 new VCFLoader(choice).loadVCF(seqs, us);
5761 chooser.showOpenDialog(null);
5767 class PrintThread extends Thread
5771 public PrintThread(AlignmentPanel ap)
5776 static PageFormat pf;
5781 PrinterJob printJob = PrinterJob.getPrinterJob();
5785 printJob.setPrintable(ap, pf);
5789 printJob.setPrintable(ap);
5792 if (printJob.printDialog())
5797 } catch (Exception PrintException)
5799 PrintException.printStackTrace();